Compositions and methods for detecting noonan syndrome

ABSTRACT

Diagnostic and therapeutic applications for Noonan Syndrome are described. The diagnostic and therapeutic applications are based on certain mutations in a RAS-specific guanine nucleotide exchange factor gene SOS1 or its expression product. The diagnostic and therapeutic applications are also based on certain mutations in a serine/threonine protein kinase gen RAF1 or its expression product thereof. Also described are nucleotide sequences, amino acid sequences, probes, and primers related to RAF1 or SOS1, and variants thereof, as well as host cells expressing such variants.

This application claims priority from U.S. Provisional Application Ser. No. 60/866,204, filed Nov. 16, 2006, which is hereby incorporated by reference in its entirety.

TECHNICAL FIELD

The present disclosure relates to diagnostic and therapeutic applications for Noonan Syndrome and, more specifically, to diagnostic and therapeutic applications based on certain mutations in RAS-specific guanine nucleotide exchange factor gene SOS1 or its expression product thereof, or certain mutations in serine/threonine protein kinase gene RAF1 or its expression product thereof.

BACKGROUND

Noonan syndrome (NS) is a developmental disorder characterized by short stature, facial dysmorphia, congenital heart defects (e.g., most commonly pulmonic stenosis and hypertrophic cardiomyopathy) and skeletal anomalies (Noonan, Am. J. Dis. Child. 116:373-80, 1968; Allanson, J. Med. Genet. 24:9-13, 1987). Other frequently associated disorders include a webbed neck, chest deformities, cryptorchidism, mental retardation, and bleeding diatheses. NS is a relatively common syndrome with an estimated incidence of 1:1000 to 1:2500 live births.

Increased RAS-mitogen-activated protein kinase (MAPK) signaling due to PTPN11 and KRAS mutations cause 50% of NS (Carta et al., Am J Hum Genet. 79:129-35, 2006; Fragale et al., Hum. Mutat. 23, 267-77, 2004; Schubbert et al., Nat Genet. 38:331-6, 2006; Tartaglia et al., Am. J. Hum. Genet. 70:1555-63, 2002; Tartaglia et al., Nat. Genet. 29:465-8, 2001). PTPN11, the first NS-associated gene identified (Tartaglia et al., 2001; see also U.S. Pat. Pub. No. 2003/0125289), encodes the non-membranous protein tyrosine phosphatase, SHP-2, that primarily serves positive regulatory roles in signal transduction, particularly via the receptor tyrosine kinase (RTK)-mediated RAS-MAPK pathway. Most mutations perturb the switch between the basally inactive and phosphotyrosine-bound active conformations of SHP-2, shifting the equilibrium towards the latter Fragale et al., 2004; Tartaglia et al., 2001; Keilhack et al., J. Biol. Chem. 280:30984-93, 2005; Tartaglia et al., Am. J. Hum. Genet. 78:279-90, 2006).

The clinical diagnosis of NS depends on recognition of the symptoms by a knowledgeable doctor. Nevertheless, substantial phenotypic variations, including mild or subtle cases, make the diagnosis difficult. Furthermore, the facial characteristics become less apparent with progressing age, so NS will sometimes remain undiagnosed. A genetic test for diagnosing Noonan syndrome involves detecting mutations in PTPN11 and KRAS, but PTPN11 and KRAS mutations account for only 50% of patients suspected of having NS. Therefore, there remains a need to identify other specific gene(s) involved in Noonan syndrome—such identification would aid in the diagnosis (in particular, early diagnosis) and treatment of a broader population of patients afflicted with NS.

SUMMARY

The present disclosure provides methods of diagnosing and treating Noonan syndrome (NS). By identifying mutations in serine/threonine protein kinase gene RAF1 in subjects with Noonan syndrome or in RAS-specific guanine nucleotide exchange factor gene SOS1, the inventors provide tools for developing genetically-based diagnostic and therapeutic applications.

In one aspect, this disclosure provides a method for diagnosing Noonan syndrome in a human subject suspected of having NS, which method comprises detecting a mutation in a RAF1 nucleic acid molecule in the subject. In certain embodiments, a mutation results in increased RAF1 activity or expression as compared to a control. The mutation can be a missense mutation, a deletion, an insertion, or a combination thereof. In other embodiments, a mutation is in a coding region of a RAF1 nucleic acid molecule, and results in a RAF1 variant polypeptide, such as a polypeptide having an amino acid substitution. In certain embodiments, a mutation in a RAF1 polypeptide is in a conserved region 2 (CR2) domain, such as amino acid substitutions at the following residues of SEQ ID NO:2: an R to S substitution at position 256; an S to L substitution at position 257; an S to F substitution at position 259; a T to R substitution at position 260; a P to S substitution at position 261; a P to R substitution at position 261; and a P to L substitution at position 261. In further embodiments, a mutation in a RAF1 polypeptide is in a CR3 domain, such as amino acid substitutions at the following residues of SEQ ID NO:2: a D to N substitution at position 486; a D to G substitution at position 486; a T to I substitution at position 491; and a T to R substitution at position 491. In still further embodiments, a mutation in a RAF1 polypeptide is in a carboxy-terminal domain, such as amino acid substitutions at the following residues of SEQ ID NO:2: an S to T substitution at position 612; and an L to V substitution at position 613.

In related embodiments, RAF1 nucleic acid molecule mutations may include nucleotide substitutions of SEQ ID NO:1 in RAF1 exon 7, exon 14, or exon 16. In certain embodiments, RAF1 nucleic acid molecule mutations in the region encoding a CR2 domain may include nucleotide substitutions at the following nucleotides of SEQ ID NO:1: a G to C substitution at position 1161; a G to T substitution at position 1161; a C to T substitution at position 1163; a C to T substitution at position 1169; a C to G substitution at position 1172; a C to T substitution at position 1174; and a C to T substitution at position 1175. In further embodiments, a mutation in a RAF1 nucleic acid molecule in the region encoding a CR3 domain may include nucleotide substitutions at the following nucleotides of SEQ ID NO:1: a G to A substitution at position 1849; an A to G substitution at position 1850; a C to T substitution at position 1865; and a C to G substitution at position 1865. In still further embodiments, a mutation in a RAF1 nucleic acid molecule in the region encoding the carboxy-terminal may include nucleotide substitutions at the following nucleotides of SEQ ID NO:1: a T to A substitution at position 2227; and a C to G substitution at position 2230.

In another aspect, this disclosure provides a method for diagnosing Noonan syndrome in a human subject suspected of having NS, which method comprises detecting a mutation in a Son of Sevenless homolog 1 (SOS1) nucleic acid molecule in the subject. In certain embodiments, a mutation results in increased SOS1 activity or expression as compared to a control. The mutation can be a missense mutation, a deletion, an insertion, or a combination thereof. In other embodiments, a mutation is in a coding region of an SOS1 nucleic acid molecule, and results in a SOS1 variant polypeptide. In one embodiment, a mutation in an SOS1 polypeptide is in an amino acid involved in autoinhibition activity wherein the autoinhibition activity is reduced as compared to wild-type SOS1 (e.g., SOS1 polypeptide of SEQ ID NO:4). In certain embodiments, a mutation in an SOS1 polypeptide is in a Pleekstrin Homology (PH) domain, such as amino acid substitutions at the following residues of SEQ ID NO:4: a W to R substitution at position 432; an E to K substitution at position 433; and a C to Y substitution at position 441. In further embodiments, a mutation in an SOS1 polypeptide is in a linker between a PH domain and a RAS exchanger motif (Rem) domain, such as amino acid substitutions at the following residues of SEQ ID NO:4: an S to R substitution at position 548; an L to P substitution at position 550; an R to G substitution at position 552; an R to K substitution at position 552; and an R to S substitution at position 552. In still further embodiments, a mutation in an SOS1 polypeptide is at an amino acid that forms part of an interacting region between a Db1 homology (DH) and a Rem domain, such as amino acid substitutions at the following residues of SEQ ID NO:4: a M to R substitution at position 269; a W to L substitution at position 729; and an Ito F substitution at position 733. In another embodiment, a mutation in an SOS1 polypeptide is in a histone folds domain, such as an E to K substitution at position 108 of SEQ ID NO:4. In still another embodiment, a mutation in an SOS1 polypeptide is in a Rem domain, such as a Y to H substitution at position 702 of SEQ ID NO:4. In yet another embodiment, a mutation in an SOS1 polypeptide is in a Cdc25 homology domain, such as an E to K substitution at position 846 of SEQ ID NO:4; or a Q to R substitution at position 977 of SEQ ID NO:4. In a further embodiment, a mutation in an SOS1 polypeptide is in the carboxy-terminal, such as an H to R substitution at position 1320 of SEQ ID NO:4. In one embodiment, an SOS1 polypeptide mutation at P655 of SEQ ID NO:4 is a polymorphism and does not correlate with NS. In yet a further embodiment, a mutant SOS1 polypeptide further comprises a deletion at position 432-433 wherein the amino acids W432 and E433 are deleted. Such an embodiment is exemplified by an R to S substitution at position 552 in combination with a W432-E433 deletion.

In related embodiments, SOS1 nucleic acid molecule mutations may include nucleotide substitutions of SEQ ID NO:1 in SOS1 exon 4, exon 7, exon 11, exon 14, exon 15, or exon 17. In certain embodiments, SOS1 nucleic acid molecule mutations in the region encoding a PH domain may include nucleotide substitutions at the following nucleotides of SEQ ID NO:3: a T to C substitution at position 1294; a G to A substitution at position 1297; and a G to A substitution at position 1322. In further embodiments, a mutation in a SOS1 nucleic acid molecule in the region encoding a PH-Rem domain linker may include nucleotide substitutions at the following nucleotides of SEQ ID NO:3: an A to C substitution at position 1642; a T to C substitution at position 1649; an A to G substitution at position 1654; a G to A substitution at position 1655; and a G to C substitution at position 1656. In still further embodiments, a mutation in a SOS1 nucleic acid molecule that encodes an amino acid that forms part of an interacting region between a DH and a Rem domain may include nucleotide substitutions at the following nucleotides of SEQ ID NO:3: a T to G substitution at position 806; a G to T substitution at position 2186; and an A to T substitution at position 2197. In another embodiment, a mutation in an SOS1 nucleic acid molecule is in a region encoding a histone folds domain, such as a G to A substitution at position 322 of SEQ ID NO:3. In still another embodiment, a mutation in an SOS1 nucleic acid molecule is in a region encoding a Rem domain, such as a T to C substitution at position 2104 of SEQ ID NO:3. In yet another embodiment, a mutation in a SOS1 nucleic acid molecule is in a region encoding a Cdc25 homology domain, such as a G to A substitution at position 2536 of SEQ ID NO:3; an A to T substitution at position 2930 of SEQ ID NO:3; or an A to G substitution at position 2930 of SEQ ID NO:3. In a further embodiment, a mutation in an SOS1 nucleic acid molecule is in a region encoding the carboxy-terminus, such as an A to G substitution at position 3959 of SEQ ID NO:3. In particular embodiments, an SOS1 nucleic acid molecule mutation at C1964 of SEQ ID NO:3 or A2930 of SEQ ID NO:3, does not correlate with NS.

In a further aspect, this disclosure provides a method for diagnosing Noonan syndrome in a human subject suspected of having NS, which method comprises assessing the level of activity of a RAF1 or SOS1 signal transduction pathway in a human subject suspected of having NS and comparing it to the level of activity in a control subject, wherein increased activity of the pathway in the subject suspected of having NS compared to the control subject is indicative of Noonan syndrome. The level of activity of the pathway can, for example, be assessed by assessing an increase in the level of activity or expression of a RAF1 or SOS1 polypeptide. Alternatively, the level of activity of the pathway can be assessed by measuring an increase in the level of activity or expression of an ERK protein, such as, e.g., ERK2. The level of activity or expression of the ERK protein may be assessed by assessing kinase activity, as described herein.

In still a further aspect, this disclosure provides a kit for diagnosing Noonan syndrome in a human subject suspected of having NS, comprising an oligonucleotide that specifically hybridizes to or adjacent to a site of mutation of a RAF1 nucleic acid sequence that results in increased activity of a RAF1 or polypeptide encoded by such a mutated nucleic acid sequence, and instructions for use. The site of RAF1 mutations may, for example, be found at nucleotide 1161, 1163, 1169, 1172, 1174, 1175, 1849, 1850, 1865, 2227, or 2230 of SEQ ID NO:1. In a further embodiment, the kit comprises at least one probe comprising the site of mutation. In another embodiment, the kit comprises a first oligonucleotide primer comprising at least 15 consecutive nucleotides of SEQ ID NO:5, and a second oligonucleotide primer comprising at least 15 consecutive nucleotides of a sequence complementary to SEQ ID NO:5. In still another embodiment, the kit comprises a first oligonucleotide primer comprising at least about 10 and up to about 30 consecutive nucleotides of SEQ ID NO:5, and a second oligonucleotide primer comprising at least about 10 and up to about 30 consecutive nucleotides of a sequence complementary to SEQ ID NO:5.

In yet a further aspect, this disclosure provides a kit for diagnosing Noonan syndrome in a human subject suspected of having NS, comprising an oligonucleotide that specifically hybridizes to or adjacent to a site of mutation of an SOS1 nucleic acid sequence that results in increased activity of an SOS1 polypeptide encoded by such a mutated nucleic acid sequence, and instructions for use. The site of SOS1 mutations may, for example, be found at nucleotide 322, 806, 1294, 1297, 1322, 1642, 1649, 1654, 1655, 1656, 2104, 2186, 2197, 2536, 2930, and 3959 of SEQ ID NO:3. In a further embodiment, the kit comprises at least one probe comprising the site of mutation. In another embodiment, the kit comprises a first oligonucleotide primer comprising at least 15 consecutive nucleotides of SEQ ID NO:6, and a second oligonucleotide primer comprising at least 15 consecutive nucleotides of a sequence complementary to SEQ ID NO:6. In still another embodiment, the kit comprises a first oligonucleotide primer comprising at least about 10 and up to about 30 consecutive nucleotides of SEQ ID NO:6, and a second oligonucleotide primer comprising at least about 10 and up to about 30 consecutive nucleotides of a sequence complementary to SEQ ID NO:6.

In yet a further aspect, this disclosure further provides a kit for diagnosing Noonan syndrome in a human subject suspected of having NS, comprising an antibody that specifically recognizes a mutation in a RAF1 or SOS1 polypeptide, and instructions for use. In certain embodiments, the mutation results in RAF1 or SOS1 polypeptide variant having an increased activity as compared to a wild-type RAF1 having an amino acid sequence of SEQ ID NO:2 or to a wild-type SOS1 having an amino acid sequence of SEQ ID NO:4, respectively. In certain embodiments, an antibody specifically binds to a RAF1 or SOS1 polypeptide variant, wherein the RAF1 or SOS1 polypeptide variant is as described herein.

In another aspect, this disclosure also provides for a method for diagnosing Noonan syndrome in a subject, which method comprises assessing the level of expression or activity of a RAF1 or SOS1 polypeptide variant in a human subject suspected of having NS and comparing to the level of expression or activity in a control subject, wherein an increased expression or basal activity of the RAF1 polypeptide in the subject suspected of having NS compared to the control subject is indicative of Noonan syndrome. The level of expression may, for example, be assessed by determining the amount of mRNA that encodes a RAF1 or SOS1 polypeptide in a biological sample or by determining the concentration of RAF1 or SOS1 polypeptide in a biological sample. The level of activity may, for example, be assessed by determining the level of RAF1 or SOS1 activity in the subject suspected of having NS.

This disclosure further provides a method for treating Noonan syndrome in a patient, which method comprises administering to the patient in need of such treatment an effective amount of an agent that modulates the expression or activity of a RAF1 or SOS1 variant polypeptide. In certain embodiments, the therapeutic agent is provided with a pharmaceutically acceptable carrier or diluent. In some embodiments, although not necessarily, the therapeutic agent is a wild-type RAF1 or SOS1 polypeptide comprising the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4, respectively. In one embodiment, the agent is a RAF1 antisense nucleic acid, preferably an antisense nucleic acid hybridizing to a segment of SEQ ID NO:1 comprising at least one nucleotide substitution as described herein. In one embodiment, the agent is a SOS1 antisense nucleic acid, preferably an antisense nucleic acid hybridizing to a segment of SEQ ID NO:3 comprising at least one nucleotide substitution as described herein.

In a specific embodiment, an agent inhibits RAF1 or SOS1 activity by blocking a RAF1 or SOS1 polypeptide variant activity, such as blocking upregulated RAS-MAPK signaling. For example, the agent can be an anti-RAF1 or an anti-SOS1 inhibitory antibody. Such an antibody could specifically recognize a RAF1 or SOS1 amino acid sequence comprising a mutation as described herein.

In a further aspect, this disclosure provides for an isolated RAF1 or SOS1 polypeptide variant comprising a mutation resulting in increased level of RAF1 or SOS1 activity. In particular embodiments, the isolated RAF1 or SOS1 polypeptide variants comprise an amino acid substitution as described herein.

This disclosure also provides an isolated nucleic acid encoding any of the RAF1 or SOS1 polypeptide variants described herein, as well as isolated oligonucleotides that specifically hybridize to such nucleic acids. This disclosure further provides for an isolated cell comprising a vector, which vector comprises a nucleic acid encoding any RAF1 or SOS1 polypeptide variant described herein, the nucleic acid operatively associated with an expression control sequence. In certain embodiments, the cell can be, for example, a prokaryotic cell or a eukaryotic cell.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic drawing showing the functional domains of the RAF1 polypeptide, including three Conserved Region domains (CR1, CR2, CR3) and a carboxy-terminal domain, are shown below. Above the schematic, the location of a Ras binding domain (RBD) and a cysteine-rich domain (CRD) within CR1 is shown, and the location of an Activation Segment within CR3 is shown. The first tier below the schematic shows the serines (S), threonine (T), and tyrosine (Y) that can be phosphorylated. The second tier below the schematic indicates the location of residues altered in Noonan syndrome.

FIGS. 2A and 2B show a two-dimensional SOS1 domain structure and location of residues altered in Noonan syndrome, and the location of mutated residues on a three-dimensional illustration of SOS1. (A) The predicted amino acid substitutions from the 14 SOS1 missense mutations are positioned below the cartoon of the SOS1 protein with its functional domains indicated above. Abbreviations: DH, Db1 homology domain; PH, Pleckstrin homology domain; Rem, RAS exchanger motif. (B) The functional domains are color coded as follows: DH, gray; PH, brown; PH-Rem helical linker, yellow; Rem, magenta; Cdc25, cyan. Residues affected by mutations are indicated with their lateral chains and numbered.

FIGS. 3A and 3B show RAS activation assays—HA-tagged wild-type SOS1 (WT), SOS1 variant R552G, and SOS1 variant W729L were individually expressed in Cos-1 cells with HA-RAS. Binding of RAS to RAF-RBD was assayed to assess RAS activation in serum-starved cells (0 min) and after 5, 15 and 30 min of EGF stimulation. (A) Total RAS and SOS1 proteins in the whole cell lysates (WCL), shown in the lower two panels, and activated RAS, upper panel, were detected immunologically with anti-HA. All fold activation ratios were compared to SOS-WT at 0 min. (B) Relative fold increase in RAS activation over basal WT SOS1, averaged from three replicates. Results from the mutants were compared to wild type at the same time points using one-tailed T-tests. Significant differences of p<0.05 are indicated with *.

FIGS. 4A and 4B show ERK activation assays—full-length, HA-tagged wild-type SOS1 (WT), SOS1 variant R552G, and SOS1 variant W729L SOS1 were individually expressed in Cos-1 cells with HA-ERK2. The fraction of ERK that was phosphorylated was assayed to assess ERK activation in serum-starved cells. (A) Total SOS1 proteins in the WCL, shown in the lowest panel, were detected with anti-HA. Total ERK and phosphoERK (pERK) in the HA immunoprecipitates were detected with anti-ERK and anti-pERK antibodies in the middle and upper panels, respectively. (B) Relative fold increase in ERK activation basally over untransfected cells, averaged from three replicates. Results for the mutants were compared to WT using one-tailed T-tests. Significant differences of p<0.01 are indicated with **.

FIGS. 5A to 5C show (A) messenger RNA, (B) genomic, and (C) protein sequences of RAF1.

FIGS. 6A to 6C show (A) messenger RNA, (B) genomic, and (C) protein sequences of SOS1.

DETAILED DESCRIPTION

The present disclosure is, in part, based on the identification of mutations in RAS-specific guanine nucleotide exchange factor gene SOS1, which are causative for or closely associated with Noonan Syndrome (NS). In another aspect, the present disclosure pertains to mutations in serine/threonine protein kinase gene RAF1, which are causative for or closely associated with Noonan Syndrome (NS). In particular, the instant disclosure provides mutant SOS1 or RAF1 coding and non-coding nucleotide sequences associated with NS. The disclosure further provides SOS1 or RAF1 polypeptides that are encoded by such variant nucleic acids or comprise one or more amino acid residue substitutions, insertions, or deletions. In certain embodiments, the SOS1 or RAF1 polypeptide variants are characterized by a gain-of-function, i.e., an increase activity over basal levels; or by higher SOS1 or RAF1 expression levels, as compared to controls.

This disclosure also provides antibodies that specifically bind to these variant SOS1 or RAF1 polypeptides, as well as nucleic acids which may be used in the methods of this disclosure to detect a variant SOS1 or RAF1 nucleic acid. For example, in one embodiment, this disclosure provides oligonucleotides sequences which may be used, e.g., to detect a mutation in a SOS1 or RAF1 nucleic acid sequence, or to amplify a SOS1 or RAF1 nucleic acid molecule (for example, a specific locus on a SOS1 or RAF1 gene) having or suspected of having a mutation that correlates to or is indicative of NS.

Methods are also provided, as part of the present disclosure, in which nucleic acids, polypeptides and antibodies described herein are used to diagnose or treat NS. For example, this disclosure provides methods to evaluate individuals suspected of having NS (e.g., clinically showing phenotypic signs of NS) by detecting a variant SOS1 or RAF1 nucleic acid molecule or SOS1 or RAF1 polypeptide, respectively, such as one of the variants described herein, that statistically correlate to NS. This disclosure further provides methods to evaluate individuals suspected of having NS by detecting an increased level of activity in the SOS1 or RAF1 signaling pathway, for example, by comparing SOS1 or RAF1 or ERK2 activity to controls. In addition, this disclosure provides therapeutic methods for treating NS by administering a compound that modulates (e.g., enhances or inhibits) the expression or activity of either an SOS1 or a RAF1 nucleic acid molecule (e.g., a SOS1 or RAF1 gene) or an SOS1 or a RAF1 gene product (e.g., an SOS1 or RAF1 polypeptide). In one preferred embodiment, the compound modulates the activity of a variant SOS1 or RAF1 nucleic acid molecule or expression product thereof, such as one of the gain-of-function variants described herein.

By way of background and as set forth above, 50% of NS cases are a result of mutations in PTPN11 and KRAS genes (Carta et al., 2006; Tartaglia et al., 2001; U.S. Pat. Pub. No. 2003/0125289). Because other genetic causes of NS are not as prevalent as PTPN11 mutations, there are not as many or as extensive familial cohorts to examine for correlation of mutations to NS, as well as a way to examine penetrance of such mutations. Accordingly, in addition to the more rare familial cases of non-PTPN11/KRAS NS, parental genotypes were used to verify sporadic cases of NS. In particular, the instant disclosure describes the analysis of nucleic acid sequences that encode polypeptides with distinct roles in RAS-MAPK signaling—in particular, RAF1 and SOS1. Example I describes mutation screening in a cohort of human subjects, in which bi-directional sequencing of all RAF1 coding exons and their flanking intronic boundaries revealed mutations that form three identifiable clusters: one in conserved region 2 (CR2); one in conserved region 3 (CR3); and one at the carboxy-terminal domain. As used herein, “carboxy-terminal domain” refers to the final 50-75 amino acids nearest the carboxy-terminus of a polypeptide. Similar sequencing analysis of SOS' revealed mutations that form three identifiable clusters: one in the Pleckstrin Homology (PH) domain; one in the linker between the PH domain and the (Rem) domain; and one at sites that form interacting regions between the Db1 homology (DH) and RAS exchanger motif (Rem) domain (i.e., functional mutations). These clustered sequence changes in RAF1 and SOS1 were absent in control individuals. Example 2 describes activity analysis of the RAF1 and SOS1 protein mutants. Example 3 describes the identification of additional mutations and further characterization of the role of the identified mutations in Noonan syndrome. Taken together, these findings establish RAF1 and SOS1 as NS disease genes.

Prior to setting forth this disclosure in more detail, it may be helpful to an understanding thereof to provide definitions of certain terms to be used herein.

Any concentration ranges recited herein are to be understood to include concentrations of any integer within that range and fractions thereof, such as one tenth and one hundredth of an integer, unless otherwise indicated. Also, any number range recited herein relating to any physical feature (such as number of nucleotides or amino acids), or size or thickness is to be understood to include any integer within the recited range, unless otherwise indicated. It should be understood that the terms “a” and “an” as used herein refer to “one or more” of the enumerated components. As used herein, the term “about” or “consisting essentially of” means±15% of a particular value, range or structure. As used herein, the terms “include” and “comprise” are used synonymously. The use of the alternative (e.g., “or”) should be understood to mean either one, both or any combination thereof of the alternatives.

As used herein, “autoinhibition” refers to proteins or polypeptides that have autoinhibitory domains that negatively regulate the function of other domains via intramolecular or intermolecular interactions. Autoinhibition can be inhibited or reduced or counteracted by mutations, proteolysis, post-translational modifications, other proteins, small molecules, and the like. For example, SOS1 is guanine nucleotide exchange factor, which has a catalytic site and an allosteric site, and its activity is regulated by autoinhibition. The basal catalytic output of SOS1 is autoinhibited by two other SOS1 domains—Db1 homology (DH) domain and Pleckstrin homology (PH) domain that form a DH-PH unit that mediates a blockade of the allosteric site, as described further herein. In another example, RAF1 is autoinhibited when the amino-terminal portion of RAF1 interacts with and inactivates the kinase domain at the carboxy-terminus. This autoinhibited conformation is stabilized by 14-3-3 protein dimers that bind to phosphorylated Ser259 and Ser621 of RAF1. In certain embodiments, autoinhibition of RAF1 or SOS1 is reduced or inhibited or counteracted by mutations as described herein.

(a) Noonan Syndrome (NS)

As used herein, the term “Noonan syndrome” or “NS” refers to disorders and diseases described under Accession No. OMIM 163950 (see the Online Mendelian Inheritance in Man (OMIM) database at www.ncbi.nlm.nih.gov/Omim, as of Nov. 13, 2006) and which are correlated to, associated with, or caused by a mutation in an SOS1or RAF1 nucleic acid molecule, or a variant SOS1 or RAF1 polypeptide. Thus, the present disclosure takes into consideration that NS and its related disorders share some phenotypical features, but are genetically heterogeneous. In a preferred embodiment, NS has a mutation in an SOS1 or RAF1 nucleic acid molecule that encodes a gain-of-function variant SOS1 or RAF1 polypeptide, respectively. NS may be correlated to, associated with, or caused by a familial form or a sporadic form, such as by mutations in an SOS1 or RAF1 nucleic acid molecule as described herein.

The phenotypic features of NS have been well described and a clinical scoring system devised. See, Mendez and Opitz, Am. J. Med. Genet. 21:493-506, 1985; Noonan, Clin. Pediatr. (Phila) 33:548-555, 1994; Sharland et al., Arch. Dis. Child 67:178-183, 1992; Duncan et al., Am. J. Med. Genet. 10:37-50, 1981). But, the phenotypic features of NS can be quite varied and are similar to other disorders, such as cardio-facio-cutaneous (CFC) syndrome, LEOPARD syndrome, etc. In addition, phenotypic heterogeneity within syndromes, phenotypic overlap between syndromes, and age-related penetrance of certain features makes precise diagnosis difficult at certain ages, particularly in infants.

For purposes of clinical diagnosis, a “person suspected of having NS,” as used herein, refers to those persons having NS disorders as described under Accession No. OMIM 163950 (previously referred to as male Turner and female pseudo-Turner Syndrome, as well as Turner phenotype with normal karyotype; see OMIM No. 163950), as well as disorders similar, or related, to NS. Exemplary NS-related disorders include the Watson (OMIM No. 193520) and LEOPARD (OMIM No. 151100) Syndromes, essentially clinically indistinguishable from NS (Mendez and Opitz, Am. J. Med. Genet. 21:493-506, 1985); Costello Syndrome (OMIM No. 218040; Costello, Am. J. Med. Genet. 62:199-201, 1996; Aoki et al., Nature Genet. 37:1038-40, 2005); cardiofaciocutaneous (CFC) syndrome (OMIM No. 115150; Reynolds et al., Am. J. Med. Genet. 25:413-27, 1986; Wieczorek et al., Clin. Genet. 52:37-46, 1997; Niihori et al., Nature Genet. 38:294-96, 2006; Rodriguez-Viciana et al., Science 311:1287-90, 2006); Noonan syndrome with multiple giant-cell lesions (OMIM No. 163955; Tartaglia et al., Am. J. Hum. Genet. 70:1555-63, 2002) and/or Noonan syndrome with multiple café-au-lait spots (also known as LEOPARD syndrome, MIM 151100; Digilio et al., Am. J. Hum. Genet. 71:389-94, 2002; Legius et al., J. Med. Genet. 39:571-4, 2002); valvular sclerosis (Snellen et al., Circulation 38(1 Suppl):93-101, 1968); and idiopathic short stature (Attie, Curr. Opin. Pediatr. 12:400-4, 2000). In view of the heterogeneous phenotypes and symptoms of NS, the present disclosure provides a molecular genetic tool for verifying a preliminary clinical diagnosis of NS and, thus, provides a method for distinguishing NS from the other phenotypically-related diseases or disorders.

The subject to whom the diagnostic or therapeutic applications of this disclosure are directed may be any human or animal, more particularly a mammal, preferably a primate or a rodent, and including monkeys, dogs, cats, horses, cows, pigs, sheep, goats, rabbits, guinea pigs, hamsters, mice and rats. In a preferred embodiment, the person suspected of having NS is a human. In other embodiments, the subject may be of any age (e.g., an adult, a child, an infant), which includes prenatal diagnostics and therapeutics interventions.

(b) RAF1

RAF1, also known as CRAF, KRAF, and MIL, is a member of the family of serine/threonine protein kinases (Wellbrock et al., Nat. Rev. Mol. Cell. Biol. 5:875-85, 2004). By way of background, mammalian genomes contain three related RAF genes, which encode ARAF, BRAF, and RAF1 (also known as CRAF), respectively. BRAF, which is archetypal, has the highest MEK (ERK kinase) activity and relatively simpler regulation (Wellbrock et al., 2004). In contrast, ARAF and RAF1 have complex regulation, which may include activation by BRAF. Complete loss of Raf1 in mice is embryonic lethal, although cells appear to have intact Ras-Mapk signaling (Huser et al., Embo J. 20:1940-51, 2001; Mikula et al., Embo J. 20:1952-62, 2001). To date, mutations in RAF1 have not been observed in human disease (OMIM No. 164760, www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM; see also Catalogue of Somatic Mutations in Cancer at www.sanger.ac.uk/genetics/CGP/cosmic/).

As used herein, the term “RAF1” in italicized form refers to a nucleic acid sequence (genomic, mRNA, cDNA, etc.), whereas the non-italicized form refers to a polypeptide or protein sequence.

In one aspect of the present disclosure, the RAF1 gene organization and intron boundary sequences are identified based on known genomic (found within GenBank Accession No. NT_(—)022517; i.e., at 12,600,108 bp-12,680,678 by from pter on chromosome 3 (3p25.2)—SEQ ID NO:5) and cDNA sequences (Genbank Accession No. NM_(—)002880; nucleotide and amino acid sequences represented herein as SEQ ID NOS:1 and 2, respectively). In the context of the present disclosure, a RAF1 gene encompasses a nucleic acid molecule of human origin, comprising a coding nucleotide sequence set forth in SEQ ID NO:1, or homologs thereof, including allelic variants and orthologs.

“RAF1 variant” nucleic acid molecules are RAF1 genomic DNA, cDNA, or mRNA comprising at least one mutation, preferably a nucleotide substitution. The nucleotide substitution may be in a coding or non-coding region. In certain embodiments, RAF1 variants are those encoding RAF1 variants having increased RAF1 activity (i.e., “gain-of-function” variants), or those that result in the expression of higher levels of RAF1 as compared to a control.

The RAF1 protein encompasses a RAF1 protein of human origin having the amino acid sequence set forth in SEQ ID NO:2, or homologs thereof, including orthologs thereof. FIG. 1 shows the organization of the functional domains of the RAF1 polypeptide, a 73 KDa multidomain polypeptide. A RAF1 polypeptide comprises three Conserved Region domains (CR1, CR2, CR3) and a carboxy-terminal domain. The CR1 includes as cysteine-rich domain (CRD) and a Ras-binding domain (RBD), and the CR3 domain includes a kinase activation segment (see FIG. 1). “RAF1 variants” refers to RAF1 proteins or polypeptides comprising at least one mutation. A RAF1 variant can be a function-conservative variant, including gain-of-function-variants, i.e., variants capable of increased RAF1 activity, such as higher serine/threonine protein kinase activity. An increase in RAF1 activity includes, for example, increased serine/threonine protein kinase activity, prolonged activity of RAF1, or a higher proportion of RAF1 remaining in an active state (e.g., dephosphorylated). This may be assessed either by direct measurement of RAF1 activity or by measuring the activity of components regulated by RAF1 activity (see Example 2). In certain embodiments, RAF1 has mutations that result in an amino acid substitution, such as those described in FIG. 1 and Table 1.

Basal level of RAF1 activity is dependent on the conformation of the protein. RAF1 is highly regulated with numerous serine (S or Ser) and threonine (T or Thr) residues that can be phosphorylated, resulting in activation or inactivation (Wellbrock et al., 2004; Dougherty et al., Mol. Cell. 17:215-24, 2005). The amino-terminal portion of RAF1 is thought to interact with and inactivate the kinase domain at the carboxy-terminus when RAF1 is in an inactive conformation. This conformation is stabilized by 14-3-3 protein dimers that bind to phosphorylated Ser259 and Ser621 (Muslin et al., Cell 84:889-97, 1996). The consensus 14-3-3 recognition sequence is R-S-X-S^(P)-X-P (Id.). Also, phosphorylation of Ser621 and subsequent 14-3-3 binding may be involved in RAF1 activation. Dephosphorylation of Ser259, which is mediated by protein phosphatase-2A (PP2A), facilitates binding of RAS-GTP at the membrane and subsequent propagation of the signal through the RAS-MAPK cascade via RAF1's MEK kinase activity. Without wishing to be bound to any specific theory, it appears that mutations associated with NS are in RAF1 amino acids that would favor an active confirmation—for example, Arg256, Ser257, Ser259, and Pro261 are all invariant residues within the 14-3-3 recognition motif of RAF1 and all were identified as mutations that correlate with or are a cause of NS (see Example 1).

An “increased activity” of RAF1 in a subject suspected of having NS or a biological sample from such a subject refers to a higher total RAF1 activity in the subject or biological sample in comparison with a control, e.g., a healthy subject or a standard sample. In certain embodiments, the RAF1 activity is at least about 10% to about 50% of a control, preferably at least about 100% to at least about 150% higher in the subject or sample than in the control. As provided by the instant disclosure, the increased activity may result from increased basal RAF1 activity, prolonged stimulation of a downstream component (e.g., ERK2 activity or RAS signaling) of an RAF1-associated pathway, and a higher RAF1 expression level. A higher RAF1 expression level may result from, for example, a mutation in a non-coding region of an RAF1 nucleic acid sequence or a mutation in a coding or non-coding gene involved in RAF1 transcription or translation. The expression level of RAF1 can be determined, for example, by comparing RAFT mRNA or levels of RAF1 protein in a subject suspected of having NS as compared to a control.

(c) SOS1

SOS1, also known as Son of Sevenless homolog 1, SOS-1, GF-1, GGF-1, GINGF, and HGF, is a member of the family of RAS-specific guanine nucleotide exchange factors and is widely expressed along with SOS2 (Bowtell et al., Proc. Nat'l. Acad. Sci. USA 89:6511-5, 1992). By way of background, one step in the activation of the RAS-MAPK pathway is the ligand-dependent conversion of RAS-GDP to RAS-GTP. In the context of receptor tyrosine kinase (RTK) signaling, this reaction is catalyzed by the RAS-specific guanine nucleotide exchange factor (GEF) Son of Sevenless (SOS) (Nimnual and Bar-Sagi, Sci STKE 2002, PE36, 2002). Structural studies of SOS1, one of two human SOS proteins (the other being SOS2), indicate that basally the protein is autoinhibited due to complex regulatory intra- and inter-molecular interactions (Corbalan-Garcia et al., Mol. Cell Biol. 18:880-6, 1998; Sondermann et al., Proc. Nat'l. Acad. Sci. USA 102, 16632-7, 2005; Sondermann et al., Cell 119:393-405, 2004). Following RTK stimulation, SOS1 is recruited to the plasma membrane where it acquires a catalytically active conformation through an as-yet ill-defined mechanism.

As used herein, the term “SOS1” in italicized form refers to a nucleic acid sequence (genomic, mRNA, cDNA, etc.), whereas the non-italicized form refers to a polypeptide or protein sequence.

In one aspect of the present disclosure, the SOS1 gene organization and intron boundary sequences are identified based on known genomic (found within GenBank Accession No. NT_(—)022184; i.e., at 39,066,469 bp-39,201,067 by from pter on chromosome 2 (2p22.1)—SEQ ID NO:6) and cDNA sequences (Genbank Accession No. NM_(—)005633; nucleotide and amino acid sequences represented herein as SEQ ID NOS:3 and 4, respectively). In the context of the present disclosure, an SOS1 gene encompasses a nucleic acid molecule of human origin, comprising a coding nucleotide sequence set forth in SEQ ID NO:3, or homologs thereof, including allelic variants and orthologs.

The SOS1 protein encompasses an SOS1 protein of human origin having the amino acid sequence set forth in SEQ ID NO:4, or homologs thereof, including orthologs thereof. FIG. 2A shows the organization of the functional domains of the SOS1 polypeptide, a 150 KDa multidomain polypeptide. An SOS1 polypeptide comprises a histone folds domain, a Db1 Homology (DH) domain, a Pleckstrin Homology (PH) domain, a RAS exchanger motif (Rem), a PH-Rem helical linker, a CDC25 homology (Cdc25) domain, and a praline rich Grbs binding domain (PxxP).

“SOS1 variant” nucleic acid molecules are SOS1 genomic DNA, cDNA, or mRNA comprising at least one mutation, preferably a nucleotide substitution. The nucleotide substitution may be in a coding or non-coding region. In certain embodiments, SOS1 variants are those encoding SOS1 variants having increased SOS1 activity (i.e., “gain-of-function” variants), or those that result in the expression of higher levels of SOS1 as compared to a control.

“SOS1 variants” are SOS1 proteins or polypeptides comprising at least one mutation. The SOS1 variants can be function-conservative variants, including gain-of-function-variants, i.e., variants capable of increased SOS1 activity, such as higher guanine nucleotide exchange activity or reduced autoinhibition activity. An increase in SOS1 activity includes, for example, increased guanine nucleotide exchange activity, prolonged activity of SOS1, or a higher proportion of SOS1 remaining in an active state (e.g., reduced autoinhibition activity). This may be assessed either by direct measurement of SOS1 activity or by measuring the activity of components regulated by SOS1 activity (see, Example 4). In certain embodiments, SOS1 has mutations that result in an amino acid substitution, such as those described in FIG. 2 and Table 2.

Basal level of SOS1 activity is dependent on the conformation of the protein. The GEF activity of SOS1 is principally controlled by two regulatory determinants: a catalytic site that forms a stable interaction with nucleotide-free RAS, and an allosteric site that potentiates exchange activity through the binding of nucleotide-bound RAS (Margarit et al., Cell 112:685-95, 2003). Whereas the former is located entirely within the Cdc25 domain, the allosteric site is bracketed by the Cdc25 domain and Rem domains. Basally, the catalytic output of SOS 1 is constrained by the DH-PH unit (Corbalan-Garcia et al., 1998), and structural data indicate that this autoinhibitory effect is exerted through DH-PH-mediated blockade of the allosteric site (Sondermann et al., 2004). Without wishing to be bound to any specific theory, it appears that the SOS1 mutations observed in Noonan syndrome are in residues that contribute to autoinhibition, either by stabilizing the interaction of the histone folds with the PH-Rem linker or interaction of the DH domain with the Rem domain, so it is believed that the predominant pathogenetic mechanism may be a release of autoinhibition followed by an enhanced GEF activity and, as a consequence, increased RAS-GTP levels (see Example 2).

An “increased activity” of SOS1 in a subject suspected of having NS or a biological sample from such a subject refers to a higher total SOS1 activity in the subject or biological sample in comparison with a control, e.g., a healthy subject or a standard sample. In certain embodiments, the SOS1 activity is at least about 10% to about 50% higher in the subject or sample than in a control, and preferably at least about 100% to at least about 150% higher in the subject or sample than in a control. As provided by the instant disclosure, the increased activity may result from increased basal SOS1 activity, prolonged stimulation of a downstream component (e.g., ERK2 activity or RAS signaling) of an SOS1-associated pathway, and a higher SOS1 expression level. A higher SOS1 expression level may result from, for example, a mutation in a non-coding region of an SOS1 nucleic acid sequence or a mutation in a coding or non-coding gene involved in SOS1 transcription or translation. The expression level of SOS1 can be determined, for example, by comparing SOS1 mRNA or levels of SOS1 protein in a subject suspected of having NS as compared to a control.

(d) RAS-MAPK Signaling Pathway

As set forth above, RAF1 and SOS1 participate in the RAS-MAPK signaling cascade. In certain embodiments, a “RAF1 signaling pathway” or “SOS1 signaling pathway” refers to a RAS-MAP kinase pathway (ERK1/2). Briefly, transmission of stimulatory signals from Ras to nuclear targets involves regulation of the family of kinases known as MAPKs (“mitogen-activated protein kinases”) or ERKs (“extracellular signal regulated kinases”). This pathway includes, but is not limited to, components such as RAF1, SOS1, and ERK2. Additional components of this pathway have been identified and described (see, e.g., Lee and McCubrey, Leukemia 16:486-507, 2002).

An “up regulation” or “increased activity” of a RAF1 or an SOS1 signaling pathway such as the RAS-MAPK pathway herein means a detectable change in signaling flux or output of the pathway that could also result from a gain-of-function RAF1 or SOS1 mutant. In certain embodiments, examples of output signals include an increased RAF1 or SOS1 activity, or increased ERK2 kinase activity. See Example 2 and FIG. 4.

(e) Molecular Biology Terms

In accordance with the present disclosure there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual, Second Edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (herein “Sambrook et al., 1989”); DNA Cloning: A Practical Approach, Volumes I and II (D. N. Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed. 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. (1985)); Transcription And Translation (B. D. Hames & S. J. Higgins, eds. (1984)); Animal Cell Culture (R. I. Freshney, ed. (1986)); Immobilized Cells And Enzymes (IRL Press, (1986)); B. Perbal, A Practical Guide To Molecular Cloning (1984); F. M. Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (1994).

The terms “polypeptide” and “protein” may be used herein interchangeably to refer to the gene product (or corresponding synthetic product) of a RAF1 or SOS1 nucleic acid molecule. The term “protein” may also refer specifically to the polypeptide as expressed in cells.

A “RAF1 gene” or “SOS1 gene,” as used herein, refers to a portion of a DNA molecule that includes a RAF1 or an SOS1 polypeptide coding sequence, respectively, operably linked to one or more expression control sequences. Thus, a gene includes both transcribed and untranscribed regions. The transcribed region may include introns, which are spliced out of the mRNA, and 5′- and 3′-untranslated (UTR) sequences along with protein coding sequences. In one embodiment, the gene can be a genomic or partial genomic sequence, in that it contains one or more introns. In another embodiment, the term gene may refer to a cDNA molecule (i.e., the coding sequence lacking introns). In yet another embodiment, the term gene may refer to expression control sequences, such as the promoter or the enhancer sequence.

A “promoter sequence” is a nucleic acid regulatory region capable of binding RNA polymerase and initiating transcription of a downstream (3′ direction) coding sequence. For purposes of the present disclosure, the promoter sequence is bounded at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. Within the promoter sequence will be found a transcription initiation site (conveniently defined for example, by mapping with nuclease S1), as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase.

“Sequence-conservative variants” of a polynucleotide sequence are those in which a change of one or more nucleotides in a given codon position results in no alteration in the amino acid encoded at that position.

“Function-conservative variants” are those in which a given amino acid residue in a protein or enzyme has been changed without altering the overall conformation and function of the polypeptide, including replacement of an amino acid with one having similar properties (such as, for example, polarity, hydrogen bonding potential, acidic, basic, hydrophobic, aromatic, and the like). Amino acids with similar properties are well known in the art. For example, arginine, histidine and lysine are hydrophilic-basic amino acids and may be interchangeable. Similarly, isoleucine, a hydrophobic amino acid, may be replaced with leucine, methionine or valine. Such changes are expected to have little or no effect on the apparent molecular weight or isoelectric point of the protein or polypeptide.

Amino acids other than those indicated as conserved may differ in a protein or enzyme so that the percent protein or amino acid sequence identity between any two proteins of similar function may vary and may be, for example, from about 70% to about 99% as determined according to an alignment scheme, such as by the Cluster Method, wherein percent identity between sequences is based on the MEGALIGN algorithm. A “variant” also includes a polypeptide or enzyme that has at least about 60% amino acid identity as determined by BLAST or FASTA algorithms, preferably at least about 75%, most preferably at least about 85%, and even more preferably at least about 90%, and still more preferably at least about 95%, and which has the same or substantially similar properties or functions as the native or parent protein or enzyme to which it is compared. In certain embodiments, a variant is a “gain-of-function” variant, meaning a polypeptide variant in which the change of at least one given amino acid residue in a protein or enzyme improves a specific function of the polypeptide, including protein activity. The change in amino acid residue can be replacement of an amino acid with one having similar properties (such as, for example, polarity, hydrogen bonding potential, acidic, basic, hydrophobic, aromatic, and the like) or different properties, or may be due to a deletion or insertion or a combination thereof.

As used herein, the term “homologous” in all its grammatical forms and spelling variations refers to the relationship between proteins that possess a “common evolutionary origin,” including proteins from superfamilies (e.g., the immunoglobulin superfamily) and homologous proteins from different species (e.g., myosin light chain, etc.) (Reeck et al., Cell 50:667, 1987). Such proteins (and their encoding genes) have sequence homology, as reflected by their sequence similarity, whether in terms of percent identity or the presence of specific amino acids or motifs at conserved positions.

Accordingly, the term “sequence similarity” or “sequence identity” in all their grammatical forms refers to the degree of identity or correspondence between nucleic acid or amino acid sequences of proteins that may or may not share a common evolutionary origin (see Reeck et al., supra). However, in common usage and in the instant application, the term “homologous,” when modified with an adverb such as “highly,” may refer to sequence similarity and does not necessarily relate to a common evolutionary origin.

In a specific embodiment, two DNA sequences are “substantially homologous” or “substantially identical” when at least about 80%, and most preferably at least about 90 or at least about 95%) of the nucleotides match over the defined length of the DNA sequences, as determined by sequence comparison algorithms, such as BLAST, FASTA, DNA Strider, etc. An example of such a sequence is an allelic or species variant of a RAF1 or SOS1 nucleic acid molecule. Sequences that are substantially homologous can be identified by comparing the sequences using standard software available in sequence data banks, or in a Southern hybridization experiment under, for example, stringent conditions as defined for that particular system.

Similarly, in a particular embodiment, two amino acid sequences are “substantially homologous” or “substantially identical” when greater than about 80% of the amino acids are identical, or greater than about 90% or about 95% are similar (functionally identical). In certain embodiments, the similar or homologous sequences are identified by alignment using, for example, the GCG (Genetics Computer Group, Program Manual for the GCG Package, Version 7, Madison, Wis.) pileup program using the default parameters, or using any of the programs described herein (BLAST, FASTA, etc.).

A nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and solution ionic strength (see Sambrook et al.). The conditions of temperature and ionic strength determine the “stringency” of the hybridization. For preliminary screening for homologous nucleic acids, low stringency hybridization conditions, corresponding to a T_(m) (melting temperature) of 55° C., can be used, e.g., 5×SSC, 0.1% SDS, 0.25% milk, and no formamide; or 30% formamide, 5×SSC, 0.5% SDS). Moderate stringency hybridization conditions correspond to a higher T_(m), e.g., 40% formamide, with 5× or 6×SCC. High stringency hybridization conditions correspond to the highest T_(m), e.g., 50% formamide, 5× or 6×SCC. SCC is a 0.15M NaCl, 0.015M Na-citrate. Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of T_(m) for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher T_(m)) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating T_(m) have been derived (see Sambrook et al., supra, 9.50-9.51). For hybridization with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8). A minimum length for a hybridizable nucleic acid is at least about 10 nucleotides; preferably at least about 15 nucleotides; and more preferably the length is at least about 20 nucleotides.

In a specific embodiment, the term “standard hybridization conditions” refers to a T_(n), of 55° C., and utilizes conditions as set forth above. In a preferred embodiment, the T_(m) is 60° C.; in a more preferred embodiment, the T_(m) is 65° C. In a specific embodiment, “high stringency” refers to hybridization or washing conditions at 68° C. in 0.2×SSC, at 42° C. in 50% formamide, 4×SSC, or under conditions that afford levels of hybridization equivalent to those observed under either of these two conditions.

The terms “mutant” and “mutation” mean any detectable change in genetic material, e.g., DNA, or any process, mechanism, or result of such a change. When compared to a control material, such change may be referred to as a “variant” or an “abnormality”. This includes gene mutations, in which the structure (e.g., DNA or RNA sequence) of a gene is altered, arising from any mutation process, and any expression product (e.g., protein or enzyme) expressed by such a modified gene or DNA sequence. The term “variant” may also be used to indicate a modified or altered gene, DNA sequence, enzyme, cell, etc., i.e., any kind of mutant.

“Amplification” of DNA as used herein encompasses the use of polymerase chain reaction (PCR) to increase the concentration of a particular DNA sequence within a mixture of DNA sequences. For a description of PCR, see Saiki et al., Science 239:487, 1988.

“Sequencing” of a nucleic acid includes chemical or enzymatic sequencing. “Chemical sequencing” of DNA denotes methods such as that of Maxam and Gilbert (Maxam-Gilbert sequencing, Maxam and Gilbert, Proc. Nat'l. Acad. Sci. USA 74:560, 1977), in which DNA is randomly cleaved using individual base-specific reactions. “Enzymatic sequencing” of DNA denotes methods such as that of Sanger (Sanger et al., Proc. Nat'l. Acad. Sci. USA 74:5463, 1977), in which a single-stranded DNA is copied and randomly terminated using DNA polymerase, including variations thereof, which are well-known in the art. Preferably, oligonucleotide sequencing is conducted using automatic, computerized equipment in a high-throughput setting, for example, microarray technology, as described herein. Such high-throughput equipment are commercially available, and techniques well known in the art.

The term “polymorphism” refers, generally, to the coexistence of more than one form of a gene (e.g., more than one allele) within a population of individuals and is not necessarily associated or correlated with a disorder or disease. The different alleles may differ at one or more positions of their nucleic acid sequences, which are referred to herein as “polymorphic locuses”. When used herein to describe polypeptides that are encoded by different alleles of a gene, the term “polymorphic locus” also refers to the positions in an amino acid sequence that differ among variant polypeptides encoded by different alleles. Polymorphisms include “single nucleotide polymorphisms” (SNPs), referring to a polymorphic site occupied by a single nucleotide, which is the site of variation between allelic sequences. Typically, the polymorphic site of an SNP is flanked by highly conserved sequences (e.g., sequences that vary in less than 1/100 and, more preferably, in less than 1/1000 individuals in a population). The polymorphic locus of an SNP may be a single base deletion, a single base insertion, or a single base substitution. Single base substitutions are particularly preferred.

As used herein, “sequence-specific oligonucleotides” refers to related sets of oligonucleotides that can be used to detect variations or mutations in a RAF1 or SOS1 gene.

A “probe” refers to a nucleic acid or oligonucleotide that forms a hybrid structure with a sequence in a target region due to complementarity of at least one sequence in the probe with a sequence in the target protein.

As used herein, the term “oligonucleotide” refers to a nucleic acid, generally of at least 10, preferably at least 15, and more preferably at least 20 nucleotides, preferably no more than 100 nucleotides, that is hybridizable to a genomic DNA molecule, a cDNA molecule, or an mRNA molecule encoding a gene, mRNA, cDNA, or other nucleic acid of interest. Oligonucleotides can be labeled, e.g., with ³²P-nucleotides or nucleotides to which a label, such as biotin, has been covalently conjugated. In one embodiment, a labeled oligonucleotide can be used as a probe to detect the presence of a nucleic acid. In another embodiment, oligonucleotides (one or both of which may be labeled) can be used as PCR primers, either for cloning full length or a fragment of RAF1 or SOS1, or to detect the presence of nucleic acids encoding RAF1 or SOS1, respectively. In a further embodiment, an oligonucleotide of this disclosure can form a triple helix with a RAF1 or SOS1 nucleic acid molecule. In still another embodiment, a library of oligonucleotides arranged on a solid support, such as a silicon wafer or chip, can be used to detect various mutations of interest. Generally, oligonucleotides are prepared synthetically, preferably on a nucleic acid synthesizer. Accordingly, oligonucleotides can be prepared with non-naturally occurring phosphoester analog bonds, such as thioester bonds, etc.

Representative examples of synthetic oligonucleotides envisioned for this disclosure include oligonucleotides that contain phosphorothioates, phosphotriesters, methyl phosphonates, short chain alkyl, or cycloalkyl intersugar linkages or short chain heteroatomic or heterocyclic intersugar linkages. Most preferred are those with CH₂—NH—O—CH₂, CH₂—N(CH)₃—O—CH₂, CH₂—O—N(CH)₃—CH₂, CH₂—N(CH)₃—N(CH)₃—CH₂ and O—N(CH)₃—CH₂—CH₂ backbones (where the phosphodiester is O—PO₂—O—CH₂). U.S. Pat. No. 5,677,437 describes heteroaromatic oligonucleoside linkages. Nitrogen linkers or groups containing nitrogen can also be used to prepare oligonucleotide mimics (U.S. Pat. No. 5,792,844 and No. 5,783,682). U.S. Pat. No. 5,637,684 describes phosphoramidate and phosphorothioamidate oligomeric compounds. Also envisioned are oligonucleotides having morpholino backbone structures (U.S. Pat. No. 5,034,506). In other embodiments, such as the peptide-nucleic acid (PNA) backbone, the phosphodiester backbone of the oligonucleotide may be replaced with a polyamide backbone, the bases being bound directly or indirectly to the aza nitrogen atoms of the polyamide backbone (Nielsen et al., Science 254:1497, 1991). Other synthetic oligonucleotides may contain substituted sugar moieties comprising one of the following at the 2′ position: OH, SH, SCH₃, F, OCN, O(CH₂)_(n)NH₂ or O(CH₂)_(n)CH₃ where n is from 1 to about 10; C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl; Cl; Br; CN; CF₃; OCF₃; O—; S—, or N-alkyl; O—, S—, or N-alkenyl; SOCH₃; SO₂CH₃; ONO₂; NO₂; N₃; NH₂; heterocycloalkyl; heterocycloalkaryl; aminoalkylamino; polyalkylamino; substituted silyl; a fluorescein moiety; an RNA cleaving group; a reporter group; an intercalator; a group for improving the pharmacokinetic properties of an oligonucleotide; or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties. Oligonucleotides may also have sugar mimetics such as cyclobutyls or other carbocyclics in place of the pentofuranosyl group. Nucleotide units having nucleosides other than adenosine, cytidine, guanosine, thymidine and uridine, such as inosine, may be used in an oligonucleotide molecule.

The present disclosure provides antisense nucleic acids (including ribozymes), which may be used to inhibit expression of a RAFT or SOS1 variant. An “antisense nucleic acid” or a “small interfering RNA” (siRNA) is a single stranded nucleic acid molecule which, on hybridizing under cytoplasmic conditions with complementary bases in an RNA or DNA molecule, inhibits the latter's role. If the RNA is a messenger RNA transcript, the antisense or siRNA nucleic acid is a countertranscript or mRNA-interfering complementary nucleic acid. As presently used, “antisense” broadly includes RNA-RNA interactions, RNA-DNA interactions, ribozymes and RNase-H mediated arrest. Antisense nucleic acid molecules can be encoded by a recombinant gene for expression in a cell (e.g., U.S. Pat. No. 5,814,500; U.S. Pat. No. 5,811,234), or alternatively they can be prepared synthetically (e.g., U.S. Pat. No. 5,780,607). Synthetic oligonucleotides are suitable for antisense use.

The terms “vector”, “cloning vector” and “expression vector” mean the vehicle by which a DNA or RNA sequence (e.g., a RAF1 or SOS1 encoding nucleic acid sequence) can be introduced into a host cell under conditions and for a time sufficient to allow expression of the introduced sequence (e.g., transcription and translation). Vectors include plasmids, phages, viruses, yeast artificial chromosomes, or the like.

The term “linkage” refers to the tendency of genes, alleles, loci or genetic markers to be inherited together as a result of their location on the same chromosome. Linkage may be measured, e.g., by the percent recombination between two genes, alleles, loci or genetic markers.

Expression of RAF1 and SOS1 Polypeptides

A nucleic acid molecule that encodes RAF1 or SOS1, or that encodes an antigenic fragment, derivative or analog of RAF1 or SOS1, or a functionally active derivative of RAF1 or SOS1 (including a chimeric protein) may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted protein-coding sequence. Thus, a nucleic acid encoding a RAF1 or SOS1 polypeptide variant of this disclosure can be operably linked to a promoter in an expression vector of this disclosure. Both cDNA and genomic sequences can be cloned and expressed under control of such regulatory sequences. Such vectors can be used to express functional or functionally inactivated RAF1 or SOS1 polypeptides. In particular, the RAF1 or SOS1 nucleic acids which may be cloned and expressed according to these methods include wild-type RAF1 or SOS1 nucleic acid molecules, as well as mutant or variant RAF1 or SOS1 nucleic acid molecules. These variants include, for example, a RAF1 or SOS1 nucleic acid having one or more of the mutations or polymorphisms set forth in Tables 1 and 2, respectively. In addition, nucleic acids that encode a variant RAF1 or SOS1 polypeptide, such as a variant RAF1 or SOS1 polypeptide comprising one or more of the amino acid substitutions listed in Tables 1 and 2, respectively, may be cloned and expressed according to the methods described here.

The necessary transcriptional and translational signals can be provided on a recombinant expression vector. Potential host-vector systems include mammalian cell systems transfected with expression plasmids or infected with virus (e.g., vaccinia virus, adenovirus, adeno-associated virus, herpes virus, etc.); insect cell systems infected with virus (e.g., baculovirus); microorganisms such as yeast containing yeast vectors; or bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA. The expression elements of vectors vary in their strengths and specificities. Depending on the host-vector system utilized, any one of a number of suitable transcription and translation elements may be used.

Expression of a RAF1 or SOS1 polypeptide may be controlled by any promoter or enhancer element known in the art, but these regulatory elements must be functional in the host selected for expression. Promoters that may be used to control RAF1 or SOS1 gene expression include a cytomegalovirus (CMV) promoter (U.S. Pat. Nos. 5,385,839 and 5,168,062), an SV40 early promoter region (Benoist and Chambon, Nature 290:304-10, 1981), a promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto et al., Cell 22:787-97, 1980), a herpes thymidine kinase promoter (Wagner et al., Proc. Nat'l. Acad. Set. U.S.A. 78:1441-5, 1981), regulatory sequences of the metallothionein gene (Brinster et al., Nature 296:39-42, 1982); prokaryotic expression vectors such as the β-lactamase promoter (VIIIa-Komaroff et al., Proc. Nat'l. Acad. Sci. U.S.A. 75:3727-31, 1978), or the tac promoter (DeBoer et al., Proc. Nat'l. Acad. U.S.A. 80:21-25, 1983); see also “Useful proteins from recombinant bacteria” in Scientific American 242:74-94, 1980. Still other useful promoter elements which may be used include promoter elements from yeast or other fungi such as the Gal 4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase) promoter, alkaline phosphatase promoter; and transcriptional control regions that exhibit hematopoietic tissue specificity, in particular: beta-globin gene control region which is active in myeloid cells (Mogram et al., Nature 315:338-340, 1985; Kollias et al., Cell 46:89-94, 1986), hematopoietic stem cell differentiation factor promoters, erythropoietin receptor promoter (Maouche et al., Blood 15:2557, 1991), etc.

Soluble forms of the protein can be obtained by collecting culture fluid, or solubilizing-inclusion bodies, e.g., by treatment with detergent, and if desired sonication or other mechanical processes, as described above. The solubilized or soluble protein can be isolated using various techniques, such as polyacrylamide gel electrophoresis (PAGE), isoelectric focusing, 2 dimensional gel electrophoresis, chromatography (e.g., ion exchange, affinity, immunoaffinity, and sizing column chromatography), centrifugation, differential solubility, immunoprecipitation, or by any other standard technique for the purification of proteins.

A wide variety of host/expression vector combinations may be employed in expressing the DNA sequences of this disclosure. Useful expression vectors, for example, may consist of segments of chromosomal, non chromosomal and synthetic DNA sequences. Suitable vectors include derivatives of SV40 and known bacterial plasmids, e.g., E. coli plasmids col E1, pCR1, pBR322, pMal-C2, pET, pGEX (Smith et al., Gene 67:31-40, 1988), pCR2.1 and pcDNA 3.1+ (Invitrogen, Carlsbad, Calif.), pMB9 and their derivatives, plasmids such as RP4; phage DNAs, e.g., the numerous derivatives of phage 1, e.g., NM989, and other phage DNA, e.g., M13 and filamentous single stranded phage DNA; yeast plasmids such as the 2 m plasmid or derivatives thereof; vectors useful in eukaryotic cells, such as vectors useful in insect or mammalian cells; vectors derived from combinations of plasmids and phage DNAs, such as plasmids that have been modified to employ phage DNA or other expression control sequences; and the like.

In certain embodiments, vectors can be viral vectors, such as lentiviruses, retroviruses, herpes viruses, adenoviruses, adeno-associated viruses, vaccinia virus, baculovirus, and other recombinant viruses with desirable cellular tropism. Thus, a gene encoding a functional or mutant RAF1 or SOS1 polypeptide or domain fragment thereof can be introduced in vivo, ex vivo, or in vitro using a viral vector or through direct introduction of a nucleic acid molecule. Expression in targeted tissues can be effected by targeting the transgenic vector to specific cells, such as with a viral vector or a receptor ligand, or by using a tissue-specific promoter, or both. Targeted gene delivery is described in International Patent Publication WO 95/28494, published October 1995.

Viral vectors commonly used for in vivo or ex vivo targeting and therapy procedures (see below), as well as in vitro expression, are DNA-based vectors and retroviral vectors. Methods for constructing and using viral vectors are known in the art (see, e.g., Miller and Rosman, BioTechniques 1992, 7:980-990). Preferably, the viral vectors are replication defective, that is, they are unable to replicate autonomously in the target cell. In general, the genomes of the replication defective viral vectors which are used within the scope of the present disclosure lack at least one region which is necessary for the replication of the virus in the infected cell. These regions can either be eliminated (in whole or in part), or can be rendered non-functional by any technique known to a person skilled in the art. These techniques include the total removal, substitution (by other sequences, in particular by the inserted nucleic acid), partial deletion or addition of one or more bases to an essential (for replication) region. Such techniques may be performed in vitro (on the isolated DNA) or in situ, using the techniques of genetic manipulation or by treatment with mutagenic agents. Preferably, the replication defective virus retains the sequences of its genome which are necessary for encapsidating the viral particles.

DNA viral vectors include an attenuated or defective DNA virus, such as but not limited to herpes simplex virus (HSV), papillomavirus, Epstein Barr virus (EBV), adenovirus, adeno-associated virus (AAV), baculovirus, and the like. RNA viral vectors include, for example, retroviruses, lentiviruses, and alphaviruses (e.g., Sindbis virus and Venezuelan Equine Encephalitis virus), and the like. Defective viruses, which entirely or almost entirely lack viral genes, are preferred. Defective virus is not infective after introduction into a cell. Use of defective viral vectors allows for administration to cells in a specific, localized area, without concern that the vector can infect other cells. Thus, a specific tissue can be specifically targeted. Examples of particular vectors include, but are not limited to, a defective herpes virus 1 (HSV1) vector (Kaplitt et al., Molec. Cell. Neurosci. 2:320-330, 1991), defective herpes virus vector lacking a glyco-protein L gene (Patent Publication RD 371005 A), or other defective herpes virus vectors (International Patent Publication No. WO 94/21807, published Sep. 29, 1994; International Patent Publication No. WO 92/05263, published Apr. 2, 1994); an attenuated adenovirus vector, such as the vector described by Stratford-Perricaudet et al. (J. Clin. Invest. 90:626-30, 1992; see also La Salle et al., Science 259:988-90, 1993); and a defective adeno-associated virus vector (Samulski et al., J. Viral. 61:3096-3101, 1987; Samulski et al., J. Viral. 63:3822-8, 1989; Lebkowski et al., Mol. Cell. Biol. 8:3988-96, 1988).

Various companies produce viral vectors commercially, including but by no means limited to Avigen, Inc. (Alameda, Calif.; AAV vectors), Cell Genesys (Foster City, Calif.; retroviral, adenoviral, AAV vectors, and lentiviral vectors), Clontech (retroviral and baculoviral vectors), Genovo, Inc. (Sharon Hill, Pa.; adenoviral and AAV vectors), Genvec (adenoviral vectors), IntroGene (Leiden, Netherlands; adenoviral vectors), Molecular Medicine (retroviral, adenoviral, AAV, and herpes viral vectors), Norgen (adenoviral vectors), Oxford BioMedica (Oxford, United Kingdom; lentiviral vectors), Transgene (Strasbourg, France; adenoviral, vaccinia, retroviral, and lentiviral vectors) and Invitrogen (Carlsbad, Calif.).

In another embodiment, the vector can be introduced in vivo by lipofection, as naked DNA, or with other transfection facilitating agents (peptides, polymers, etc.). Synthetic cationic lipids can be used to prepare liposomes for in vivo transfection of a gene encoding a marker (Felgner et al., Proc. Nat'l. Acad, Sci. U.S.A. 1987, 84:7413-7417; Felgner and Ringold, Science 337:387-88, 1989; Mackey et al., Proc. Nat'l. Acad. Sci. U.S.A. 85:8027-31, 1988; Ulmer et al., Science 259:1745-48, 1993). Useful lipid compounds and compositions for transfer of nucleic acids are described in International Patent Publications WO 95/18863 and WO 96/17823, and in U.S. Pat. No. 5,459,127. Lipids may be chemically coupled to other molecules for the purpose of targeting (see Mackey et al., Proc. Nat'l. Acad. Sci. U.S.A. 85:8027-31, 1988). Targeted peptides, and proteins such as antibodies, or non-peptide molecules could be coupled to liposomes chemically. Other molecules are also useful for facilitating transfection of a nucleic acid in vivo, such as a cationic oligopeptide (e.g., International Patent Publication WO 95/21931), peptides derived from DNA binding proteins (e.g., International Patent Publication WO 96/25508), or a cationic polymer (e.g., International Patent Publication WO 95/21931).

It is also possible to introduce the vector in vivo as a naked DNA plasmid. Naked

DNA vectors for gene therapy can be introduced into the desired host cells by methods known in the art; e.g., electroporation, microinjection, cell fusion, DEAE dextran, calcium phosphate precipitation, use of a gene gun, or use of a DNA vector transporter (see, e.g., Wu et al., J. Biol. Chem. 1992, 267:963-967; Wu and Wu, J. Biol. Chem. 1988, 263:14621-14624; Hartmut et al., Canadian Patent Application No. 2,012,311, filed Mar. 15, 1990; Williams et al., Proc. Nat'l. Acad. Sci. U.S.A. 1991, 88:2726-2730). Receptor-mediated DNA delivery approaches can also be used (Curiel et al., Hum. Gene Ther. 1992, 3:147-154; Wu and Wu, J. Biol. Chem. 1987, 262:4429-4432). U.S. Pat. Nos. 5,580,859 and 5,589,466 disclose delivery of exogenous DNA sequences, free of transfection facilitating agents, in a mammal. Recently, a relatively low voltage, high efficiency in vivo DNA transfer technique, termed electrotransfer, has been described (Mir et al., C.P. Acad. Sci. 1998, 321:893; WO 99/01157; WO 99/01158; WO 99/01175).

Preferably, for in vivo administration, an appropriate immunosuppressive treatment is employed in conjunction with the viral vector, e.g., adenovirus vector, to avoid immuno-deactivation of the viral vector and transfected cells. For example, immunosuppressive cytokines, such as interleukin-12 (IL-12), interferon-γ (IFN-γ), or anti-CD4 antibody, can be administered to block humoral or cellular immune responses to the viral vectors (see, e.g., Wilson, Nat. Med. 1:887-9, 1995). In that regard, it is advantageous to employ a viral vector that is engineered to express a minimal number of antigens.

Diagnostic Methods

According to the present disclosure, mutated forms of RAF1 and 5051 can be detected to diagnose a subject suspected of having Noonan syndrome. For example, detection of RAF1 or SOS1 mutants that encode RAF1 or SOS1 polypeptide variants, respectively, can function as a “genetic diagnostic” to verify a preliminary clinical diagnosis based on known phenotypic NS characteristics.

Accordingly, diagnostic methods may comprise, for example, detecting a mutation in a RAF1 or SOS1 nucleic acid molecule, wherein the mutation results in increased RAF1 or SOS1 polypeptide activity, respectively. In certain embodiments, mutations may affect a coding region, such as conserved region 1 (CR1), CR2, CR3, or the carboxy-terminus of RAF1. In other embodiments, mutations may affect an SOS1 coding region, such as a Pleckstrin Homology-Ras Exchanger motif (PH-Rem) linker, PH domain, or amino acids involved in associating Db1 Homology (DH) domain with the Rem domain. The mutations may be a missense mutation, preferably a missense mutation resulting in a nucleic acid substitution, or a deletion, or a combination thereof. In certain embodiments, the mutation results in one or more of the amino acid substitutions set forth in Table for Table 2.

The diagnostic methods of this disclosure also encompass detecting a mutation in a RAF1 or SOS1 polypeptide, in particular a mutation that results in increased activity of the RAF1 or SOS1 polypeptide. In one embodiment, the RAF1 or SOS1 mutation is an amino acid substitution. In certain embodiments, the RAF1 mutation is in the CR1, CR2, CR3, or the carboxy-terminus domain, including domains involved in 14-3-3 protein binding. In certain related embodiments, amino acid substitutions of RAF1 are set forth in Table 1. In other embodiments, the SOS1 mutation is in a PH-Rem linker, a PH domain, or amino acids involved in associating a DH domain with a Rem domain. In further related embodiments, amino acid substitutions of SOS1 are set forth in Table 2.

In another embodiment, the diagnosis of Noonan syndrome in a subject suspected of having NS comprises assessing the level of activity or expression of RAF1 or SOS1 protein and comparing it to the level of activity or expression in a control subject, wherein an increased activity or expression of the RAF1 or SOS1 protein in the subject compared to the control subject is indicative of Noonan syndrome.

The level of expression of RAF1 or SOS1 may be assessed by determining the amount of mRNA that encodes the RAF1 or SOS1 protein, respectively, in a biological sample, or by determining the concentration of RAF1 or SOS1 protein in a biological sample. The level of RAF1 or SOS1 protein or activity may be assessed by determining the level of serine/threonine protein kinase activity or guanine nucleotide exchange activity, respectively, in a sample or subject, and the level of activity in a RAF1 or SOS1 signaling pathway may be assessed by determining the pathway signaling flux, e.g., by measuring RAF1 or SOS1 or ERK activity in a sample or subject, as described herein.

This disclosure also provides kits for performing these diagnostic methods. In one embodiment of this disclosure, a kit is provided for diagnosing Noonan syndrome in a human suspected of having NS, comprising an oligonucleotide that specifically hybridizes to a site harboring a mutation of a RAF1 or SOS1 nucleic acid molecule, or hybridizes to an adjacent site, wherein the mutation results in increased basal activity of the RAF1 or SOS1 protein. In certain embodiments, a RAF1 mutation may comprise a nucleotide substitution at nucleotide 1161, 1163, 1169, 1172, 1174, 1175, 1849, 1850, 1865, 2227, or 2230 of SEQ ID NO:1 (see Table 1), as described herein. In certain other embodiments, an SOS1 mutation may comprise a nucleotide substitution at nucleotide 322, 806, 1294, 1297, 1322, 1642, 1649, 1654, 1655, 1656, 2104, 2186, 2197, 2536, 2930, 3959 of SEQ ID NO:3 (see Table 2), as described herein. A further subject of this disclosure is a kit for diagnosing Noonan syndrome in a human suspected of having NS, comprising an antibody that specifically recognizes a variant form of a RAF1 or SOS1 polypeptide, which variants have an increased basal activity of RAF1 or SOS1 polypeptide, respectively.

As used herein, the term “diagnosis” refers to the identification of the disease at any stage of its development, and also includes the determination of a predisposition of a subject to develop the disease. In certain aspects, this disclosure peg nits genetic counseling of prospective parents and in utero genetic testing for Noonan syndrome. Families with one affected parent or with advanced paternal age are of particular concern. The diagnostic method of this disclosure also allows confirmation of a questionable NS diagnosis based on phenotype (appearance and symptomology). The diagnostic method of this disclosure may also be envisioned in the case of fetal abnormalities whose cause may not be obvious, or in the case of fetal loss, to evaluate viability of future pregnancies.

The term “biological sample” refers to any cell source from which a nucleic acid molecule may be obtained. Exemplary cell sources available in clinical practice include blood cells, buccal cells, cervicovaginal cells, epithelial cells from urine, fetal cells, or any cells present in tissue obtained by biopsy. Cells may also be obtained from body fluids, including without limitation blood, plasma, serum, lymph, milk, cerebrospinal fluid, saliva, sweat, urine, feces, and tissue exudates (e.g., pus) at a site of infection or inflammation. For prenatal testing, genetic material can be obtained from fetal cells, e.g., from amniotic fluid (through amniocentesis), chronic villi, blood, or any tissue of a pregnant woman. DNA is extracted using any of the numerous methods that are standard in the art. It will be understood that the particular method used to extract DNA will depend on the nature of the source. Generally, the minimum amount of DNA to be extracted for use in the present disclosure is about 25 pg (corresponding to about 5 cell equivalents of a genome size of 4×10⁹ base pairs). Various methods for detecting such mutated forms of a RAF1 or SOS1 polypeptide are described herein.

The present disclosure further contemplates detecting abnormalities, i.e., mutations in a RAF1 or SOS1 nucleic acid sequence, that result in an increased basal activity of an encoded RAF1 or SOS1 polypeptide, respectively; result in a constitutively active polypeptide; provide prolonged and increased RAF1 or SOS1 polypeptide activity; or increase the level of expressed RAF1 or SOS1 polypeptide.

Mutations may include an insertion, a truncation, a deletion, a nonsense mutation, a frameshift mutation, a splice-site mutation, or a missense mutation. Such mutations can occur in the coding region of a RAF1 or SOS1 nucleic acid sequence, more particularly in any of the identified structural or functional domains, as well as in the untranslated regions, such as a promoter or enhancer region. In certain embodiments, RAF1 nucleic acid molecule mutations are nucleotide substitutions of SEQ ID NO:1 in RAF1 exon 7, exon 14, or exon 16. In other embodiments, SOS1 nucleic acid molecule mutations are nucleotide substitutions of SEQ ID NO:3 in SOS1 exon 4, exon 7, exon 11, exon 14, exon 15, or exon 17. In preferred embodiments, RAF1 or SOS1 mutations result in amino acid substitutions, such as those listed in Table 1 and Table 2, respectively.

Nucleic Acid Based Assays

According to this disclosure, mutated forms of RAF1 or SOS1 nucleic acids, i.e., in the RAF1 or SOS1 DNA or their transcripts, respectively, as well as deregulated expression, e.g., overexpression of RAF1 or SOS1 or other components of a RAF1 or SOS1 signaling pathway (e.g., ERK2) can be detected by a variety of suitable methods.

Standard methods for analyzing the nucleic acid contained in a biological sample and for diagnosing a genetic disorder can be employed, and many strategies for genotypic analysis are known to those of skill in the art.

In one embodiment, the detection of mutations in the RAF1 or SOS1 gene encompasses the use of nucleic acid sequences, such as specific oligonucleotides, to detect mutations in RAF1 or SOS1 genomic DNA or mRNA in a biological sample. Such oligonucleotides may be specifically hybridized at a site of mutation or at a region adjacent to the site of mutation present in a RAF1 or SOS1 nucleic acid molecule. One may also employ primers that permit amplification of all or part of a RAF1 or SOS1 nucleic acid molecule. Alternatively, or in combination with such techniques, oligonucleotide sequencing described herein or known to the skilled artisan can be applied to detect RAF1 or SOS1 mutations.

One skilled in the art may use hybridization probes in solution and in embodiments employing solid-phase procedures. In embodiments involving solid-phase procedures, the test nucleic acid is adsorbed or otherwise affixed to a selected matrix or surface. The fixed, single-stranded nucleic acid is then subjected to specific hybridization with selected probes.

In another embodiment, one skilled in the art may use oligonucleotide primers in an amplification technique, such as PCR or reverse-PCR (“reverse polymerase chain reaction”), to specifically amplify the target DNA or mRNA, respectively, which is potentially present in the biological sample.

In certain embodiments, the instant disclosure provides oligonucleotides, such as primers that permit amplification of SOS1 exons. Exemplary SOS1 primers include the following sequences:

Exon 1 (SOS1): Forward primer: (SEQ ID NO: 7) 5′- TCCACGGCTGGTACCTGTGTC -3′ Reverse primer: (SEQ ID NO: 8) 5′- ACCGAGAGCCAGCCGTATGAG -3′ Exon 2 (SOS1): Forward primer: (SEQ ID NO: 9) 5′- GGTGGTCTCAAACTCCTGACC -3′ Reverse primer: (SEQ ID NO: 10) 5′- ACTTCTGTTCCCAAGCATTCTGG -3′ Exon 3 (SOS1): Forward primer: (SEQ ID NO: 11) 5′- ATTATACCACATGTGAAAAGCTC -3′ Reverse primer: (SEQ ID NO: 12) 5′- TTCTCACCACATAAATCTCTGG -3′ Exon 4 (SOS1): Forward primer: (SEQ ID NO: 13) 5′- AAATGTTGTTGGTAAGCACAGGC -3′ Reverse primer: (SEQ ID NO: 14) 5′- TCCCTACTATTAGGTTACTGGAG -3′ Exon 5 (SOS1): Forward primer: (SEQ ID NO: 15) 5′- AACTTTATTCAGAGAACTTAGAGC -3′ Reverse primer: (SEQ ID NO: 16) 5′- GGTCATGCAAATTTCACAACAC -3′ Exon 6 (SOS1): Forward primer: (SEQ ID NO: 17) 5′- CACTGACCTAGAGAAATGTATTTGC -3′ Reverse primer: (SEQ ID NO: 18) 5′- TAGCTGGAAAGAAGTAAGACTCTC -3′ Exon 7/8 (SOS1): Forward primer: (SEQ ID NO: 19) 5′- AATTGTGCTCGCATAGTCGTGC -3′ Reverse primer: (SEQ ID NO: 20) 5′- CTAATGTGCAGGGTACTCACAC -3′ Exon 9 (SOS1): Forward primer: (SEQ ID NO: 21) 5′- CTTAACACTGCTAATCTTGGTC -3′ Reverse primer:  (SEQ ID NO: 22) 5′- CTTCATTGTTTACTTGAGGAGG -3′ Exon 10 (SOS1): A. Forward primer: (SEQ ID NO: 23) 5′- CACTTTCCCTTACTTACATGAGCTC -3′ Reverse primer: (SEQ ID NO: 24) 5′- CTGTAAAGATATCAATGCTGCCA -3′ B. Forward primer: (SEQ ID NO: 25) 5′- GATGACACCAATGAATACAAGC -3′ Reverse primer: (SEQ ID NO: 26) 5′- CATGCAGGAAAGAAAATCAGT -3′ Exon 11 (SOS1): Forward primer: (SEQ ID NO: 27) 5′- AAGTCCAAAGCCTTCTACTTGG -3′ Reverse primer: (SEQ ID NO: 28) 5′- TGAAAAGGATCTTAGCTCAATCTC -3′ Exon 12 (SOS1): Forward primer: (SEQ ID NO: 29) 5′- GTTTACACTGATATGCATATCTTCAG -3′ Reverse primer: (SEQ ID NO: 30) 5′- CTAATTTTATTGTCACCCCTCTCC -3′ Exon 13 (SOS1): Forward primer: (SEQ ID NO: 31) 5′- CTGATAAGATTAATTTGGTAAGAG -3′ Reverse primer: (SEQ ID NO: 32) 5′- TATAAACATCTTACATTACTGAGC -3′ Exon 14 (SOS1): Forward primer: (SEQ ID NO: 33) 5′- CAAAGATACATTCAGGTGTCATCC -3′ Reverse primer: (SEQ ID NO: 34) 5′- GTCTTATGAAAACCCTATAAGGCAG -3′ Exon 15 (SOS1): Forward primer: (SEQ ID NO: 35) 5′- TATAAGAGGAAAGTTCATATGAGAG -3′ Reverse primer: (SEQ ID NO: 36) 5′- GAAATTCATAACATAGCTGACAGC -3′ Exon 16 (SOS1): Forward primer: (SEQ ID NO: 37) 5′- GCCTTCCTTCTATCAGTCACCC -3′ Reverse primer: (SEQ ID NO: 38) 5′- TAGCTTAGGCTGGGACCTGTG -3′ Exon 17 (SOS1): Forward primer: (SEQ ID NO: 39) 5′- TGTATTTGGGCGTTTCTGTTAGCC -3′ Reverse primer: (SEQ ID NO: 40) 5′- GATCAAACAAGTATTTTCTGCTGGC -3′ Exon 18 (SOS1): Forward primer: (SEQ ID NO: 41) 5′- GATGGTACAGTGTAATATACCCAC -3′ Reverse primer: (SEQ ID NO: 42) 5′- CTTCTCCATGCTATTTCCCATCG -3′ Exon 19 (SOS1): Forward primer: (SEQ ID NO: 43) 5′- CCAAAATCAGCCTTACTGTTTACG -3′ Reverse primer: (SEQ ID NO: 44) 5′- CACATATGGTAGTAATGACATCACC -3′ Exon 20 (SOS1): Forward primer: (SEQ ID NO: 45) 5′- TATATTAGCTGAATTTTACCAGGC -3′ Reverse primer: (SEQ ID NO: 46) 5′- ACTTAACTACAAGTTCACACATAC -3′ Exon 21 (SOS1): Forward primer: (SEQ ID NO: 47) 5′- ATGAAATCAAGTAAAGCTAAAAGG -3′ Reverse primer: (SEQ ID NO: 48) 5′- CTAAAGATAGCACAAGTGAAGG -3′ Exon 22 (SOS1): Forward primer: (SEQ ID NO: 49) 5′- ATTGGTTTATTGAACAGCTTTTGG -3′ Reverse primer: (SEQ ID NO: 50) 5′- AGTGAGAACTAAACTAGACAGC -3′ Exon 23 (SOS1): A. Forward primer: (SEQ ID NO: 51) 5′- ACACTTAGCATCCTGCCAATAGC -3′ Reverse primer: (SEQ ID NO: 52) 5′- CTGTTTGGGAAGAAGGCATTGC -3′ B. Forward primer: (SEQ ID NO: 53) 5′- TCAAGCTCACCACTACATCTCC -3′ Reverse primer: (SEQ ID NO: 54) 5′- GTTCTCATTTTAACTCCTCAGTGC -3′

In certain other embodiments, the instant disclosure provides oligonucleotides, such as primers that permit amplification of RAF1 exons. Exemplary RAF1 primers include the following sequences:

Exon 2 (RAF1): (SEQ ID NO: 55) Forward primer: 5′-TCTTTGCTGATGAATGCAGGAG-3′ (SEQ ID NO: 56) Reverse primer: 5′-AATGACAATGAATATTTTGCCTGTC-3′ Exon 3 (RAF1): (SEQ ID NO: 57) Forward primer: 5′-CATCACAAGCAATACAGACTGG-3′ (SEQ ID NO: 58) Reverse primer: 5′-AACTTTTCAAGAGAATGTCCAAGC-3′ Exon 4 (RAF1): (SEQ ID NO: 59) Forward primer: 5′-AACTTGCTGTGTGGCCTTGAG-3′ (SEQ ID NO: 60) Reverse primer: 5′-TGAGAAATCTCTGTTATGCCTGG-3′ Exon 5 (RAF1): (SEQ ID NO: 61) Forward primer: 5′-GTACATGCTGGAAGTATGATTC-3′ (SEQ ID NO: 62) Reverse primer: 5′-CCTGTCAGTCAAAATCTACAAC-3′ Exon 6 (RAF1): (SEQ ID NO: 63) Forward primer: 5′-CTGTATGTTTATTGGCAGGTCAG-3′ (SEQ ID NO: 64) Reverse primer: 5′-CAGTATCAAGTTCCACAGAAGC-3′ Exon 7 (RAF1): (SEQ ID NO: 65) Forward primer: 5′-CCAGTATGAAAGCCTAAGTGC-3′ (SEQ ID NO: 66) Reverse primer: 5′-CTGAAATAAGTATCAACCTCACC-3′ Exon 8/9 (RAF1): (SEQ ID NO: 67) Forward primer: 5′-ATCTTTTGTGTGTAGGAGTTGACC-3′ (SEQ ID NO: 68) Reverse primer: 5′-TTCTTACTGAACCCTAATTGGCAG-3′ Exon 10 (RAF1): (SEQ ID NO: 69) Forward primer: 5′-CATGGGTTGATCCTTTGATGC-3′ (SEQ ID NO: 70) Reverse primer: 5′-CTTGACTTCACACCAAAGCCC-3′ Exon 11 (RAF1): (SEQ ID NO: 71) Forward primer: 5′-CACTGTATCTTCCTCAAAACTAG-3′ (SEQ ID NO: 72) Reverse primer: 5′-CAGTGAGTCCTAACTGCCTGC-3′ Exon 12 (RAF1): (SEQ ID NO: 73) Forward primer: 5′-GCTTCTCTTTGCTCAGAATGC-3′ (SEQ ID NO: 74) Reverse primer: 5′-CTGATCCTGGTTCCAATTTAGG-3′ Exon 13 (RAF1): (SEQ ID NO: 75) Forward primer: 5′-GTGGCTTTACTTCTTAGCTGTAG-3′ (SEQ ID NO: 76) Reverse primer: 5′-ACCGAGAGCCACTTGTGATAG-3′ Exon 14 (RAF1): (SEQ ID NO: 77) Forward primer: 5′-GACCATTCTTTTGAAACCAGAG-3′ (SEQ ID NO: 78) Reverse primer: 5′-GCATTCCTTTTGCCCTATACC-3′ Exon 15 (RAF1): (SEQ ID NO: 79) Forward primer: 5′-CTAGATGTCTGTGAGGCCTGTC-3′ (SEQ ID NO: 80) Reverse primer: 5′-CAAGTCCTAACCCTCTAGCTGC-3′ Exon 16 (RAF1): (SEQ ID NO: 81) Forward primer: 5′-CTAAGCAGCTAGAGGGTTAGGAC-3′ (SEQ ID NO: 82) Reverse primer: 5′-CTCCCACCTTATATTGCCATC-3′ Exon 17 (RAF1): (SEQ ID NO: 83) Forward primer: 5′-GATGGCAATATAAGGTGGGAG-3′ (SEQ ID NO: 84) Reverse primer: 5′-TCCTTAGCAGCAGCTTCTCTG-3′

The present disclosure also provides a method of in vitro diagnosis of NS in a human suspected of having NS, comprising the steps of:

(a) contacting a biological sample containing DNA with specific oligonucleotides for amplification of all or part of a RAF1 or SOS1 nucleic acid molecule;

(b) amplifying said DNA;

(c) detecting the amplification products;

(d) comparing the amplified products as obtained to the amplified products obtained with a normal control biological sample, and thereby detecting a possible abnormality in the RAF1 or SOS1 nucleic acid molecule.

The method of this disclosure can also be applied to the detection of an abnormality in the transcript of a RAF1 or SOS1 nucleic acid molecule, e.g., by amplifying the mRNAs contained in a biological sample, such as by RT-PCR.

Thus, another embodiment of the present disclosure is a method of in vitro diagnosis of NS in a human suspected of having NS, comprising the steps of:

(a) producing cDNA from mRNA contained in a biological sample;

(b) contacting said cDNA with specific oligonucleotides permitting the amplification of all or part of the transcript of the RAFT or SOS1 gene, under conditions permitting a hybridization of the primers with said cDNA;

(c) amplifying said cDNA;

(d) detecting the amplification products;

(e) comparing the amplified products as obtained to the amplified products obtained with a normal control biological sample, and thereby detecting a possible abnormality in the transcript of the RAF1 or SOS1 gene.

For RNA analysis, a biological sample may be any cell source, as described herein, such as a biopsy tissue, from which RNA is isolated using standard methods well known to those of ordinary skill in the art, including guanidium thiocyanate-phenol-chloroform extraction (Chomocyznski et al., Anal. Biochem. 162:156, 1987). The isolated RNA is then subjected to coupled reverse transcription and amplification by polymerase chain reaction (RT-PCR), using specific oligonucleotide primers that are specific for a selected site. Conditions for primer annealing are chosen to ensure specific reverse transcription and amplification; thus, the appearance of an amplification product is diagnostic of the presence of a particular genetic variation. In another embodiment, RNA is reverse-transcribed and amplified, after which the amplified sequences are identified by, e.g., direct sequencing. In still another embodiment, RAF1 or SOS1 cDNA obtained from the respective RNAs can be cloned and sequenced to identify a mutation.

The RAF1 or SOS1 nucleic acids of this disclosure can also be used as probes, e.g., in therapeutic and diagnostic assays. For instance, the present disclosure provides a probe comprising a substantially purified oligonucleotide, which oligonucleotide comprises a region having a nucleotide sequence that is capable of hybridizing specifically to a region of a RAF1 or SOS1 nucleic acid sequence that differs from the wild-type sequence (SEQ ID NO:5 or 6, respectively), e.g., a mutant or polymorphic region. Such probes can then be used to specifically detect which mutation of a RAF1 or SOS1 nucleic acid sequence is present in a sample taken from a subject, particularly a subject suspected of having NS. A mutant or polymorphic region can be located in the promoter, exon, or intron sequences of the RAF1 or SOS1 gene.

For example, certain RAF1 or SOS1 probes of this disclosure include one or more of the nucleotide substitutions listed in Table 1 or Table 2, respectively, as well as the wild-type flanking regions (see, e.g., SEQ ID NOS:1, 3, 5 and 6). For each such probe, the complement of that probe is also included as a preferred probe of this disclosure. Particularly preferred probes of this disclosure have a number of nucleotides sufficient to allow specific hybridization to the target nucleotide sequence. Thus, probes of suitable lengths based on SEQ ID NO:1, 3, 5 or 6 and complementary to the mutant RAF1 or SOS1 sequences provided herein can be constructed and tested by the skilled artisan for an appropriate level of specificity depending on the application intended. Where the target nucleotide sequence is present in a large fragment of DNA, such as a genomic DNA fragment of several tens or hundreds of kilobases, the size of the probe may have to be longer to provide sufficiently specific hybridization, as compared to a probe which is used to detect a target sequence which is present in a shorter fragment of DNA. For example, in some diagnostic methods, a portion of a RAF1 or SOS1 nucleic acid sequence may first be amplified and thus isolated from the rest of the chromosomal DNA, and then hybridized to a probe. In such a situation, a shorter probe will likely provide sufficient specificity of hybridization. For example, a probe having a nucleotide sequence of about 10 nucleotides may be sufficient, although probes of about 15 to about 20 nucleotides are preferred.

In a preferred embodiment, the probe or primer further comprises a label attached thereto, which is capable of being detected. The label can, for example, be selected from radioisotopes, fluorescent compounds, enzymes, enzyme co-factors, and the like.

In another preferred embodiment of this disclosure, the isolated nucleic acid, which is used, e.g., as a probe or a primer, is modified to be more stable. Exemplary nucleic acid molecules that are modified include phosphoramidate, phosphothioate and methylphosphonate analogs of DNA (see also U.S. Pat. Nos. 5,176,996; 5,264,564; and 5,256,775).

In yet another embodiment, one may use HPLC or denaturing HPLC (DHPLC) techniques to analyze the RAF1 or SOS1 nucleic acids. DHPLC was developed when observing that, when HPLC analyses are carried out at a partially denaturing temperature, i.e., a temperature sufficient to denature a heteroduplex at the site of base pair mismatch, homoduplexes can be separated from heteroduplexes having the same base pair length (Hayward-Lester et al., Genome Research 5:494, 1995; Underhill et al., Proc. Nat'l. Acad. Sci. USA 93:193, 1996; Doris et al., DHPLC Workshop, 1997, Stanford University), Thus, the use of DHPLC was applied to mutation detection (Underhill et al., Genome Research 7:996, 1997; Liu et al., Nucleic Acid Res. 26:1396, 1998). DHPLC can separate heteroduplexes that differ by as little as one base pair. “Matched Ion Polynucleotide Chromatography” (MIPC), or Denaturing “Matched Ion Polynucleotide Chromatography” (DMIPC) as described in U.S. Pat. No. 6,287,822 or 6,024,878, are separation methods that can also be useful in connection with the present disclosure.

Alternatively, one can use the DGGE method (Denaturing Gradient Gel Electrophoresis), or the SSCP method (Single Strand Conformation Polymorphism) for detecting an abnormality in a RAF1 or SOS1 nucleic acid molecule. DGGE is a method for resolving two DNA fragments of identical length on the basis of sequence differences as small as a single base pair change, using electrophoresis through a gel containing varying concentrations of denaturant (Guldberg et al., Nuc. Acids Res. 1994, 22:880). SSCP is a method for detecting sequence differences between two DNAs, comprising hybridization of the two species with subsequent mismatch detection by gel electrophoresis (Ravnik-Glavac et al., Hum. Mol. Genet. 3:801, 1994). “HOT cleavage”, a method for detecting sequence differences between two DNAs, comprising hybridization of the two species with subsequent mismatch detection by chemical cleavage (Cotton, et al., Proc. Nat.'l. Acad. Sci. USA 85:4397, 1988), can also be used. Such methods are preferably followed by direct sequencing. Advantageously, the RT-PCR method may be used for detecting abnormalities in a RAF1 or SOS1 transcript, as it allows one to visualize the consequences of a splicing mutation such as exon skipping or aberrant splicing due to the activation of a cryptic site. In certain embodiments, this method is followed by direct sequencing as well.

More recently developed techniques using microarrays, preferably microarray techniques allowing for high-throughput screening, can also be advantageously implemented for detecting an abnormality in a RAF1 or SOS1 nucleic acid molecule or for assaying expression of a RAF1 or SOS1 nucleic acid molecule or the gene of another component in the RAF1 or SOS1 pathway resulting in increased signaling, as described herein. Microarrays may be designed so that the same set of identical oligonucleotides is attached to at least two selected discrete regions of the array, so that one can easily compare a normal sample, contacted with one of the selected regions of the array, against a test sample, contacted with another of the selected regions. These arrays avoid the mixture of normal sample and test sample, using microfluidic conduits. Useful microarray techniques include those developed by Nanogen, Inc (San Diego, Calif.) and those developed by Affymetrix. However, all types of microarrays, also called “gene chips” or “DNA chips”, may be adapted for the identification of mutations. Such microarrays are well known in the art (see, for example, the following: U.S. Pat. Nos. 6,045,996; 6,040,138; 6,027,880; 6,020,135; 5,968,740; 5,959,098; 5,945,334; 5,885,837; 5,874,219; 5,861,242; 5,843,655; 5,837,832; 5,677,195 and 5,593,839).

The solid support on which oligonucleotides are attached may be made from glass, silicon, plastic (e.g., polypropylene, nylon), polyacrylamide, nitrocellulose, or other materials. One method for attaching the nucleic acids to a surface is by printing on glass plates, as is described generally by Schena et al., Science 1995, 270:467-470. This method is especially useful for preparing microarrays of cDNA. See also DeRisi et al., Nature Genetics 14:457-460, 1996; Shalon et al., Genome Res. 1996, 6:639-645; and Schena et al., Proc. Natl. Acad. Sci. USA 1995, 93:10539-11286. Another method of making microarrays is by use of an inkjet printing process to bind genes or oligonucleotides directly on a solid phase, as described, e.g., in U.S. Pat. No. 5,965,352.

Other methods for making microarrays, e.g., by masking (Maskos and Southern, Nuc. Acids Res. 1992, 20:1679-1684), may also be used. In principal, any type of array, for example, dot blots on a nylon hybridization membrane (see Sambrook et al., Molecular Cloning A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989) could be used, although, as will be recognized by those of skill in the art, very small arrays will be preferred because hybridization volumes will be smaller. For these assays nucleic acid hybridization and wash conditions are chosen so that the attached oligonucleotides “specifically bind” or “specifically hybridize” to at least a portion of a RAF1 or SOS1 nucleic acid molecule present in a target sample, i.e., the probe hybridizes, duplexes or binds to the RAF1 or SOS1 locus with a complementary nucleic acid sequence but does not hybridize to a site with a non-complementary nucleic acid sequence. As used herein, one polynucleotide sequence is considered complementary to another when, if the shorter of the polynucleotides is less than or equal to 25 bases, there are no mismatches using standard base-pairing rules or, if the shorter of the polynucleotides is longer than 25 bases, there is no more than a 5% mismatch. Preferably, the polynucleotides are perfectly complementary (no mismatches). It can easily be demonstrated that specific hybridization conditions result in specific hybridization by carrying out a hybridization assay including negative controls (see, e.g., Shalon et al., supra, and Chee et al., Science 274:610-4, 1996).

A variety of methods are available for detection and analysis of a hybridization event. Depending on the reporter group (fluorophore, enzyme, radioisotope, etc.) used to label a DNA probe, detection and analysis are carried out fluorimetrically, colorimetrically or by autoradiography. By observing and measuring emitted radiation, such as fluorescent radiation or a particle emission, information may be obtained about hybridization events.

When fluorescently labeled probes are used, the fluorescence emissions at each site of transcript array can, preferably be detected by scanning confocal laser microscopy. In one embodiment, a separate scan, using the appropriate excitation line, is carried out for each of the two fluorophores used. Alternatively, a laser can be used that allows simultaneous specimen illumination at wavelengths specific to the two fluorophores and emissions from the two fluorophores can be analyzed simultaneously (see Shalon et al., Genome Res. 6:639-695, 1996).

Protein Based Assays

As an alternative to analyzing RAF1 or SOS1 nucleic acids, one can evaluate RAF1 or SOS1 on the basis of mutations in the polypeptide or on the basis of dysregulated production, e.g., overproduction of the protein. In addition, RAF1 or SOS1 activity and/or ERK kinase activity can be evaluated to determine increased activity of a RAF1 or SOS1 signaling pathway such as the RAS-MAPK pathway.

In preferred embodiments, RAF1 or SOS1 or ERK2 are detected by immunoassay. For example, Western blotting permits detection of a specific variant, or the presence or absence of RAF1 or SOS1 or ERK2. In particular, an immunoassay can detect a specific (wild-type or mutant) amino acid sequence in a RAF1 or SOS1 protein. Other immunoassay formats can also be used in place of Western blotting, as described below for the production of antibodies. One of these is ELISA assay.

In ELISA assays, an antibody against RAF1 or SOS1, an epitopic fragment of RAF1 or SOS1, or ERK2, is immobilized onto a selected surface, for example, a surface capable of binding proteins such as the wells of a polystyrene microtiter plate. After washing to remove incompletely adsorbed polypeptides, a nonspecific protein such as a solution of bovine serum albumin (BSA) may be bound to the selected surface. This allows for blocking of nonspecific adsorption sites on the immobilizing surface and thus reduces the background caused by nonspecific bindings of antisera onto the surface. The immobilizing surface is then contacted with a sample, to be tested in a manner conductive to immune complex (antigen/antibody) formation. This may include diluting the sample with diluents, such as solutions of BSA, bovine gamma globulin (BGG) and/or phosphate buffered saline (PBS)/Tween. The sample is then allowed to incubate for from 2 to 4 hours, at temperatures between about 25° to 37° C. Following incubation, the sample-contacted surface is washed to remove non-immunocomplexed material. The washing procedure may include washing with a solution, such as PBS/Tween or borate buffer. Following formation of specific immunocomplexes between the test sample and the bound antibody, and subsequent washing, the occurrence, and an even amount of immunocomplex formation may be determined by subjecting the immunocomplex to a second antibody against RAF1 or SOS1 or ERK2, which recognizes a different epitope on the proteins. To provide a method of detection, a second antibody may have an associated activity such as an enzymatic activity that will generate, for example, a color development upon incubating with an appropriate chromogenic substrate. Quantification may then be achieved by measuring the degree of color generation using, for example, a visible spectra spectrophotometer.

Typically the detection antibody is conjugated to an enzyme such as peroxidase and the protein is detected by the addition of a soluble chromophore peroxidase substrate such as tetramethylbenzidine followed by 1 M sulfuric acid. The test protein concentration is determined by comparison with standard curves. These protocols are detailed in Current Protocols in Molecular Biology, V. 2 Ch. 11 and Antibodies, a Laboratory Manual, Ed Harlow, David Lane, Cold Spring Harbor Laboratory (1988) pp 579-593.

Alternatively, a biochemical assay can be used to detect expression, or accumulation of RAF1 or SOS1 or ERK2, e.g., by detecting the presence or absence of a protein band in samples analyzed by polyacrylamide gel electrophoresis; by the presence or absence of a chromatographic peak in samples analyzed by any of the various methods of high performance liquid chromatography, including reverse phase, ion exchange, and gel permeation; by the presence or absence of RAF1 or SOS1 or ERK2 in analytical capillary electrophoresis chromatography, or any other quantitative or qualitative biochemical technique known in the art.

The immunoassays discussed above involve using antibodies directed against a RAF1 or SOS1 protein or fragments thereof. The production of such antibodies is described below. Production of anti-ERK2 antibodies, or other components of a RAF1 or SOS1 pathway, can be prepared in a similar manner.

Anti-RAF1 and Anti-SOS1 Antibodies

In certain embodiment, antibodies specific for RAF1 or SOS1 are provided, which include polyclonal, monoclonal, chimeric, humanized, human, single chain, Fab fragments, Fab expression library, and the like.

Various procedures known in the art may be used for the production of polyclonal antibodies to a RAF1 or SOS1 polypeptide, or derivative or analog thereof. For the production of a polyclonal antibody, various host animals can be immunized by injection with the antigenic polypeptide, including rabbits, mice, rats, sheep, goats, etc.

Any technique that provides for the production of antibody molecules by continuous cell lines in culture may be used for the preparation of monoclonal antibodies specific for a RAF1 or SOS1 polypeptide. These methods include the hybridoma technique originally developed by Kohler and Milstein (Nature 256:495-7, 1975), as well as the trioma technique, the human B-cell hybridoma technique (Kozbor et al., Immunology Today 4:72, 1983; Cote et al., Proc. Nat'l. Acad. Sci. U.S.A. 80:2026-2030, 1983), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96, 1985). In an additional embodiment of this disclosure, monoclonal antibodies can be produced in germ-free animals (International Patent Publication No, WO 89/12690, published 28 December, 1989).

According to this disclosure, techniques described for the production of single chain antibodies (U.S. Pat. Nos. 5,476,786 and 5,132,405 to Huston; U.S. Pat. No. 4,946,778) can be adapted to produce a RAF1 or SOS1 polypeptide-specific single chain antibodies. Indeed, these genes can be delivered for expression in vivo. An additional embodiment of this disclosure utilizes the techniques described for the construction of Fab expression libraries (Huse et al., Science 246:1275-1281, 1989) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for a RAF1 or SOS1 polypeptide, or its derivatives or analogs thereof.

Antibody fragments which contain the idiotype of the antibody molecule can be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′)₂ fragment which can be produced by pepsin digestion of the antibody molecule; the Fab′ fragments which can be generated by reducing the disulfide bridges of the F(ab′)₂ fragment, and the Fab fragments which can be generated by treating the antibody molecule with papain and a reducing agent.

In the production of antibodies, screening for the desired antibody can be accomplished by techniques known in the art, e.g., radioimmunoassay, ELISA (enzyme-linked immunosorbant assay), “sandwich” immunoassays, immunoradiometric assays, gel diffusion precipitin reactions, immunodiffusion assays, in situ immunoassays (using colloidal gold, enzyme or radioisotope labels, for example), western blots, precipitation reactions, agglutination assays (e.g., gel agglutination assays, hemagglutination assays), complement fixation assays, immunofluorescence assays, protein A assays, and immunoelectrophoresis assays, etc. In one embodiment, antibody binding is detected by detecting a label on the primary antibody. In another embodiment, the primary antibody is detected by detecting binding of a secondary antibody or reagent to the primary antibody. In a further embodiment, the secondary antibody is labeled. Many means are known in the art for detecting binding in an immunoassay and are within the scope of the present disclosure.

RAF1, SOS1 and ERK2 Activity Assays

As described herein, increased activity or level of a RAF1 or SOS1 polypeptide or other components in a RAF1 or SOS1 signaling pathway is indicative of NS. In one embodiment one may assess the activity of a RAF1 or SOS1 polypeptide in a human subject or biological sample taken from the subject suspected of having NS and compare with a control. An increased activity of a RAF1 or SOS1 polypeptide in the target subject or biological sample compared with the control is indicative of NS in the target subject.

The activity of a RAF1 or SOS1 polypeptide may be indirectly assayed by evaluating the level of expression, accumulation or activity of down-stream effectors, as described herein. In certain embodiments, down-stream effectors are MAP kinases, such as ERK1 or ERK2. The nucleic acid-based assays or protein-based assays as described herein may be readily adapted for such a purpose. Since RAF1 is a kinase and SOS1 has a Ras binding domain, the basal activity of RAF1 or SOS1 polypeptide in a subject suspected of having NS may be easily determined by assessing kinase activity of RAF1 variant polypeptides and by assessing Ras activation by SOS1 variant polypeptides.

In one embodiment, the level of phosphorylation of a peptide or protein is assessed by utilizing a binding partner, which should preferably be highly specific for the phosphoepitope on the target protein. It is preferred that the binding partner is an antibody. The antibody is preferably generated against a unique epitope of the substrate. In an alternative embodiment, the binding partner should be specific for the phosphorylated form of the target protein. The detection procedure used to assess the phosphorylation state of the protein may for instance employ an antibody or a peptide that recognizes and binds to phosphorylated serines, threonines or tyrosines. The detection antibody is preferably a polyclonal antibody, to maximize the signal, but may also be specific monoclonal antibodies which have been optimized for signal generation. An exemplary kinase and Ras activation assays are provided in the Examples.

ERK activity, in particular ERK2 activity, can be assessed by measuring kinase activity, i.e., transfer of phosphate from ATP to a second substrate. Many such assays are known in the art, and an exemplary ERK2 assay is provided in Example 2. Alternatively, immunoassays may be replaced by the detection of radiolabeled phosphate according to a standard technique. This involves incubating cells with the test substances and radiolabeled phosphate, lysing the cells, separating cellular protein components of the lysate using as SDS-polyacrylamide gel (SDS-PAGE) technique, in either one or two dimensions, and detecting the presence of phosphorylated proteins by exposing X-ray film.

The phosphorylation of a protein may also be conveniently detected by migration on a gel subject to electrophoresis, followed by western blotting. Phosphorylation is detected by a shift of the molecular weight of the protein occurs, a phosphorylated protein being heavier than the corresponding non-phosphorylated form.

Diagnostic Kits

The present disclosure further provides kits for the determination of the sequence within a RAF1 or SOS1 gene in an individual. In some embodiments, the kits comprise agent(s) for determining the RAF1 or SOS1 nucleic acid sequence at the variant positions, and may optionally include data for analysis of mutations. The means for sequence determination may comprise suitable nucleic acid-based and immunological reagents. In certain embodiments, the kits also comprise suitable buffers, control reagents where appropriate, and directions for determining the sequence at a variant position.

(a) Nucleic Acid Based Diagnostic Kits

This disclosure provides nucleic acid-based methods for detecting genetic variations of RAF1 or SOS1 in a biological sample. The sequence at particular positions in a RAF1 or SOS1 gene is determined by using any suitable means known in the art, including one or more of hybridization with specific probes for PCR amplification (e.g., primer pairs selected from SEQ ID NOS:3-32), restriction fragmentation, direct sequencing, SSCP, and other techniques known in the art. The present disclosure also provides kits suitable for nucleic acid-based diagnostic applications. In one embodiment, diagnostic kits include the following components:

(a) a probe nucleic acid molecule, wherein the probe nucleic acid molecule may be pre-labeled; alternatively, the probe nucleic acid molecule may be unlabeled and the ingredients for labeling may be included in the kit in separate containers; and

(b) hybridization reagents, wherein the kit contains other suitably packaged reagents and materials needed for the particular hybridization protocol, including solid-phase matrices, if applicable, and standards.

In certain embodiments, the probe nucleic acid molecule is DNA.

In another embodiment, diagnostic kits include:

(a) Sequence determination primers: Sequencing primers may be pre-labeled or may contain an affinity purification or attachment moiety; and

(b) Sequence determination reagents: The kit may also contain other suitably packaged reagents and materials needed for the particular sequencing protocol.

In one embodiment, the kit comprises a panel of sequencing primers, whose sequences correspond to sequences adjacent to variant positions on a RAF1 or SOS1 nucleic acid molecule.

(b) Antibody-Based Diagnostic Kits

This disclosure also provides antibody-based methods for detecting mutant (or wild type) RAF1 or SOS1 polypeptides in a biological sample. The methods comprise the steps of: (i) contacting a sample with one or more antibody, wherein each antibody is specific for a mutant (or wild type) RAF1 or SOS1 polypeptide under conditions in which a stable antigen-antibody complex can form; and (ii) detecting any antigen-antibody complex formed in step (i) using any suitable means known in the art, wherein the detection of a complex indicates the presence of a mutant (or wild type) RAF1 or SOS1 polypeptide.

Generally, immunoassays use either a labeled antibody or a labeled antigenic component (e.g, that competes with the antigen in the sample for binding to the antibody). Suitable labels include enzyme-based, fluorescent, chemiluminescent, radioactive, dye molecules, or the like. Assays that amplify the signals from the probe are also known, such as, for example, those that utilize biotin and avidin, and enzyme-labeled immunoassays, such as ELISA assays.

The present disclosure also provides kits suitable for antibody-based diagnostic applications. In certain embodiments, diagnostic kits include one or more of the following components: (i) RAF1 or SOS1 polypeptide-specific antibodies, wherein the antibodies may be pre-labeled; alternatively, the antibody may be unlabeled and the ingredients for labeling may be included in the kit in separate containers, or a secondary, labeled antibody is provided; and (ii) reaction components, wherein the kit optionally contains other suitably packaged reagents and materials needed for the particular immunoassay protocol, including solid-phase matrices, if applicable, and standards.

The kits referred to above may include instructions for conducting the test. Furthermore, in preferred embodiments, the diagnostic kits are adaptable to high-throughput or automated operation.

Therapeutics

The present disclosure further provides a method for the treatment of NS, which method comprises modulating activity of a RAF1 or SOS1 polypeptide in a subject or patient having a RAF1 or SOS1 mutation. In another embodiments, the instant disclosure provides a method in which a subject suspected of having NS is diagnosed with NS by detecting a mutation in a RAF1 or SOS1 nucleic acid molecule, wherein the RAF1 or SOS1 nucleic acid molecule encodes a RAF1 or SOS1 polypeptide of SEQ ID NO:2 or 4, respectively, having an amino acid substitution and reduced autoinhibition as described herein, and the NS is treated by administering an effective amount of an agent that modulates activity of the variant RAF1 or SOS1 polypeptide. In any of these embodiments, the method comprises administering to a patient in need of such treatment an effective amount of an agent that modulates RAF1 or SOS1 polypeptide expression or activity, with a pharmaceutically acceptable diluent or carrier. For example, the therapeutic agent may be a RAF1 or SOS1 antisense or small interfering nucleic acid molecule, or an anti-RAF1 or anti-SOS1 intracellular inhibitory antibody.

In another aspect, the present disclosure further provides a method for the treatment of hypertrophic cardiomyopathy (IICM) associated with NS. In certain embodiments, a subject having HCM associated with NS is treated with an agent that modulates or alters the activity of a RAF1 polypeptide in a subject having a mutation in a RAF1 nucleic acid molecule of SEQ ID NO:1, wherein the mutated RAF1 nucleic acid molecule encodes a RAF1 variant polypeptide having an amino acid substitution and reduced autoinhibition, as described herein. In particular embodiments, the instant disclosure provides a method in which a subject, who has HCM and is suspected of having NS, is diagnosed with NS by detecting a mutation in a RAF1 nucleic acid molecule, wherein the RAF1 nucleic acid molecule encodes a RAF1 polypeptide of SEQ ID NO:2 having an amino acid substitution and reduced autoinhibition as described herein, and the NS-associated HCM is treated by administering an effective amount of an agent that modulates activity of the variant RAF1 polypeptide. In any of these embodiments, an agent that modulates RAF1 polypeptide activity in a pharmaceutically acceptable diluent or carrier is administered to the subject in need thereof. For example, the therapeutic agent may be a RAF1 antisense or small interfering nucleic acid molecule or an anti-RAF1 intracellular inhibitory antibody.

A “subject” or “patient” is a human or an animal likely to develop NS or suspected of having NS, more particularly a mammal, preferably a human or a primate as described herein in connection with diagnostic applications. Prenatal treatment is also envisioned, In a preferred embodiment, the subject is human.

The term “treatment” means to therapeutically intervene in the development of a disease in a subject showing a symptom of this disease. The term “treatment” also encompasses prevention, which means to prophylactically interfere with a pathological mechanism that results in a disease.

The term “modulating RAF1 or SOS1 activity” in a subject means modifying it so that it is rendered as close as possible to the normal RAF1 or SOS1 activity of a control subject. In certain embodiments, modulating RAF1 or SOS1 activity encompasses inhibiting or blocking the activity of a RAF1 or SOS1 variant polypeptide in an NS patient. Preferred modulators block any of the functional domains of a variant RAF1 or SOS1 polypeptide as described herein. As used herein, modulating RAF1 or SOS1 activity also encompasses increasing or restoring autoinhibition activity.

The modulation activity may be achieved by various methods, as described herein. In one embodiment, a modulatory agent may be a substance that is known or has been identified to modulate, especially inhibit, whether fully or partially, variant RAF1 or SOS1 polypeptides with gain-of function activity. For example, this modulatory agent may be a candidate drug as identified by a screening method analyzing Ras-activation or Mek kinase activity. In other embodiments, a modulatory agent may also be an inhibitory antibody directed against variant RAF1 or SOS1 polypeptides with gain-of function activity. In a further embodiment, a modulatory agent may be an antisense or small interfereing nucleic acid. A substance that modulates or inhibits RAF1 or SOS1 activity is advantageously formulated in a pharmaceutical composition, with a pharmaceutically acceptable carrier or diluent. This substance may then be called an active ingredient or therapeutic agent against NS. The pharmaceutical compositions may also include other biologically active compounds.

The team “therapeutically effective amount” as used herein means an amount or dose sufficient to modulate, e.g., decrease the level of variant RAF1 or SOS1 activity e.g., by about 10 percent, preferably by about 50 percent, and more preferably by about 90 percent. Preferably, a therapeutically effective amount can ameliorate or present a clinically significant deficit in the activity, function, and response of the subject. Alternatively, a therapeutically effective amount is sufficient to cause an improvement in a clinically indentifiable condition in a subject. The concentration or amount of an active ingredient depends on the desired dosage and administration regimen, as discussed herein. Suitable dose ranges may include from about 0.01 mg/kg to about 100 mg/kg of body weight per day.

The phrase “pharmaceutically acceptable” refers to molecular entities and compositions that are physiologically tolerable and do not typically produce an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human. Preferably, as used herein, the term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water or aqueous solution saline solutions and aqueous dextrose and glycerol solutions are preferably employed as carriers, particularly for injectable solutions. Suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin.

A composition comprising “A” (where “A” is a single protein, DNA molecule, vector, recombinant host cell, etc.) is substantially free of “B” (where “B” comprises one or more contaminating proteins, DNA molecules, vectors, etc.) when at least about 75% by weight of the proteins, DNA, vectors (depending on the category of species to which A and B belong) in the composition is “A”. Preferably, “A” comprises at least about 90% by weight of the A+B species in the composition, most preferably at least about 99% by weight. It is also preferred that a composition, which is substantially free of contamination, contain only a single molecular weight species having the activity or characteristic of the species of interest.

According to this disclosure, the pharmaceutical composition of this disclosure can be introduced parenterally, transmucosally, e.g., orally (per os), nasally, or rectally, or transdermally. Parental routes include intravenous, intra-arteriole, intra-muscular, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial administration. Targeting heart, e.g. by direct administration to heart muscle or cavities, may be advantageous.

The pharmaceutical compositions may be added to a retained physiological fluid such as blood or synovial fluid.

In another embodiment, the active ingredient can be delivered in a vesicle, in particular a liposome (see Langer, Science 249:1527-1533 (1990); Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss: New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid.).

In yet another embodiment, the therapeutic compound can be delivered in a controlled release system. For example, a polypeptide may be administered using intravenous infusion with a continuous pump, in a polymer matrix such as poly-lactic/glutamic acid (PLGA), a pellet containing a mixture of cholesterol and the active ingredient (SilasticR™; Dow Corning, Midland, Mich.; see U.S. Pat. No. 5,554,601) implanted subcutaneously, an implantable osmotic pump, a transdermal patch, liposomes, or other modes of administration.

Screening Methods

A “test substance” is a chemically defined compound or mixture of compounds (as in the case of a natural extract or tissue culture supernatant), whose ability to modulate RAF1 or SOS1 activity may be defined by various assays. A “test substance” is also referred to as a “candidate drug” in the present description.

Test substances may be screened from large libraries of synthetic or natural compounds. Numerous means are currently used for random and directed synthesis of saccharide, peptide, and nucleic acid based compounds. Synthetic compound libraries are commercially available from Maybridge Chemical Co. (Trevillet, Cornwall, UK), Comgenex (Princeton, N.J.), Brandon Associates (Merrimack, N.H.), and Microsource (New Milford, Conn.). A rare chemical library is available from Aldrich (Milwaukee, Wis.). Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available from, e.g., Pan Laboratories (Bothell, Wash.) or MycoSearch (NC), or are readily producible. Additionally, natural and synthetically produced libraries and compounds are readily modified through conventional chemical, physical, and biochemical means (Blondelle et al., TIBTech 1996, 14:60).

A modulatory effect may be determined by an in vitro method using a recombinant RAF1- or SOS1-reporter gene promoter activity system. Reporter genes for use in this disclosure encode detectable proteins, include, but are by no means limited to, chloramphenicol transferase (CAT), β-galactosidase (β-gal), luciferase, green fluorescent protein (GFP) and derivatives thereof, yellow fluorescent protein and derivatives thereof, alkaline phosphatase, other enzymes that can be adapted to produce a detectable product, and other gene products that can be detected, e.g., immunologically (by immunoassay).

A screen according to this disclosure involves detecting expression of the reporter gene by the host cell when contacted with a test substance. If there is no change in expression of the reporter gene, the test substance is not an effective modulator. If reporter gene expression is modified, in particular reduced or eliminated, the test substance has modulated, e.g., inhibited, RAF1- or SOS1-mediated gene expression, and is thus a candidate for development as an NS therapeutic.

The reporter gene assay system described here may be used in a high-throughput primary screen for antagonists, or it may be used as a secondary functional screen for candidate compounds identified by a different primary screen, e.g., a binding assay screen that identifies compounds that modulate RAF1 or SOS1 transcription activity.

Potential drugs may be identified by screening in high-throughput assays, including without limitation cell-based or cell-free assays. It will be appreciated by those skilled in the art that different types of assays can be used to detect different types of agents. Several methods of automated assays have been developed in recent years so as to permit screening of tens of thousands of compounds in a short period of time (see, e.g., U.S. Pat. Nos. 5,585,277, 5,679,582, and 6,020,141). Such high-throughput screening methods are particularly preferred. Alternatively, simple reporter-gene based cell assays such as the one described here are also highly desirable.

Intact cells or whole animals expressing a gene encoding RAF1 or SOS1 can be used in screening methods to identify candidate drugs.

In one series of embodiments, a permanent cell line is established. Alternatively, cells are transiently programmed to express a RAF1 or SOS1 gene by introduction of appropriate DNA or mRNA.

Identification of candidate substances can be achieved using any suitable assay, including without limitation (i) assays that measure selective binding of test compounds to RAF1 or SOS1 (ii) assays that measure the ability of a test substance to modify (i.e., inhibit) a measurable activity or function of RAF1 or SOS1 and (iii) assays that measure the ability of a substance to modify (i.e., inhibit) the transcriptional activity of sequences derived from the promoter (i.e., regulatory) regions of a RAF1 or SOS1 gene.

Selected agents may be modified to enhance efficacy, stability, pharmaceutical compatibility, and the like. Structural identification of an agent may be used to identify, generate, or screen additional agents. For example, where peptide agents are identified, they may be modified in a variety of ways, e.g. to enhance their proteolytic stability.

Inhibitory Antibodies

The modulatory substance may also be an antibody that is directed against RAF1 or SOS1. Antibodies that block the activity of RAF1 or SOS1 may be produced and selected according to any standard method well-known by one skilled in the art, such as those described above in the context of diagnostic applications.

Intracellular antibodies (sometime referred to as “intrabodies”) have been used to regulate the activity of intracellular proteins in a number of systems (see, Marasco, Gene Ther. 1997, 4:11; Chen et al., Hum. Gene Ther. 1994, 5:595), e.g., viral infections (Marasco et al., Hum. Gene Ther. 1998, 9:1627) and other infectious diseases (Rondon et al., Annu. Rev. Microbiol. 1997, 51:257), and oncogenes, such as p21 (Cardinale et al., FEBS Lett. 1998, 439:197-202; Cochet et al., Cancer Res. 1998, 58:1170-6), myb (Kasono et al., Biochem Biophys Res Commun. 1998, 251:124-30), erbB-2 (Graus-Porta et al., Mol Cell Biol. 1995, 15:1182-91), etc. This technology can be adapted to inhibit RAF1 or SOS1 activity by expression of an anti-RAF1 or anti-SOS1 intracellular antibody.

Antisense Therapy

In another embodiment, vectors comprising a sequence encoding an antisense nucleic acid according to this disclosure may be administered by any known methods, such as the methods for gene therapy available in the art. Exemplary methods are described below. For general reviews of the methods of gene therapy, see, Goldspiel et al., Clinical Pharmacy 1993, 12:488-505; Wu and Wu, Biotherapy 1991, 3:87-95; Tolstoshev, Ann. Rev. Pharmacol. Toxicol. 1993, 32:573-596; Mulligan, Science 1993, 260:926-932; and Morgan and Anderson, Ann. Rev. Biochem. 1993, 62:191-217; May, TIBTECH 1993, 11:155-215. Methods commonly known in the art of recombinant DNA technology that can be used are described in Ausubel et al., (eds.), 1993, Current Protocols in Molecular Biology, John Wiley & Sons, NY; Kriegler, 1990, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY; and in Chapters 12 and 13, Dracopoli et al., (eds.), 1994, Current Protocols in Human Genetics, John Wiley & Sons, NY.

In one embodiment, a vector is used in which the coding sequences and any other desired sequences are flanked by regions that promote homologous recombination at a desired site in the genome, thus providing for expression of the construct from a nucleic acid molecule that has integrated into the genome (Koller and Smithies, Proc. Nat'l. Acad. Sci. USA 86:8932-35, 1989; Zijlstra et al., Nature 342:435-38, 1989).

Delivery of the vector into a patient may be either direct, in which case the patient is directly exposed to the vector or a delivery complex, or indirect, in which case, cells are first transformed with the vector in vitro, then transplanted into the patient. These two approaches are known, respectively, as in vivo and ex vivo gene therapy.

In a specific embodiment, the vector is directly administered in vivo, where it enters the cells of the organism and mediates expression of the construct. This can be accomplished by any of numerous methods known in the art and discussed above, e.g., by constructing it as part of an appropriate expression vector and administering it so that it becomes intracellular, e.g., by infection using a defective or attenuated retroviral or other viral vector (see, U.S. Pat. No. 4,980,286), or by direct injection of naked DNA, or by use of microparticle bombardment (e.g., a gene gun; Biolistic, Dupont); or coating with lipids or cell-surface receptors or transfecting agents, encapsulation in biopolymers (e.g., poly-∃-1-64-N— acetylglucosamine polysaccharide; see, U.S. Pat. No. 5,635,493), encapsulation in liposomes, microparticles, or microcapsules; by administering it in linkage to a peptide or other ligand known to enter the nucleus; or by administering it in linkage to a ligand subject to receptor-mediated endocytosis (see, e.g., Wu and Wu, J. Biol. Chem. 62:4429-32, 1987), etc. In another embodiment, a nucleic acid-ligand complex can be formed in which the ligand comprises a fusogenic viral peptide to disrupt endosomes, allowing the nucleic acid to avoid lysosomal degradation, or cationic 12-mer peptides, e.g., derived from antennapedia, that can be used to transfer therapeutic DNA into cells (Mi et al., Mol. Therapy. 2:339-47, 2000). In yet another embodiment, the nucleic acid can be targeted in vivo for cell specific uptake and expression, by targeting a specific receptor (see, e.g., PCT Publication Nos. WO 92/06180, WO 92/22635, WO 92/20316 and WO 93/14188).

Examples of practicing this disclosure are provided, and are understood to be exemplary only, and do not limit the scope of this disclosure or the appended claims. A person of ordinary skill in the art will appreciate that this disclosure can be practiced in many forms according to the claims and disclosures herein.

EXAMPLES Example 1 Detection of Mutations in RAF1 and SOS1

High-Throughput Resequencing.

A cohort of 96 human subjects with NS was assembled from whom genomic DNAs were obtained from peripheral blood leukocytes. Nearly all subjects were Caucasian and of European ancestry, with the majority being Italian. The subjects did not harbor a PTPN11 or a KRAS mutation based on scanning of the coding exons with DHPLC (Wave 2100 System, Transgenomic) and/or bidirectional DNA sequencing as previously described (Carta et al., Am. J. Hum. Genet. 79:129-135, 2006; Tartaglia et al., Am. J. Hum. Genet. 70:1555-63, 2002). For sporadic cases, which represented the vast majority of the subjects, we obtained both parental DNAs whenever possible. All non-anonymous samples were collected under Institutional Review Board-approved protocols and with informed consent.

We chose a cohort of this size with the assumption that RAF1 and SOS1 would account for at least 1% of NS (or 2% of PTPN11-/KRAS-negative NS). Based on Collins and Schwartz (Am. J. Hum. Genet. 71:1251-2, 2002), this powered the study to detect a mutation in an NS gene at approximately 80% with α=0.05. If the gene accounted for 5% of PTPN11-/KRAS-negative NS, then the power to detect it with a cohort of this size would exceed 95%.

A high throughput approach to the resequencing of RAF1 and SOS1 was performed. The resequencing protocol was as follows: oligonucleotide primers (see Table A) for amplifying the RAF1 coding exons (n=17) and SOS1 coding exons (n=23) were designed to give a product size in the range of 200-700 by with a minimum of 40 by flanking the splice sites using the Exon Primer program (ihg.gsf.de/ihg/ExonPrimer.html), which is bundled with the UCSC Genome Browser (hg17 genome build: genorne.ucsc.edu), M13F and M13R tags were added to the forward and reverse primers, respectively. Five nanograms of genomic DNA from each NS sample was amplified in an 8 μl PCR reaction using AmpliTaq Gold (Applied Biosystems) using PE 9700 machines and subsequently cleaned using a diluted version of the Exo-SAP based PCR product pre-sequencing kit (USB Corporation) dispensed by a nanoliter dispenser (Deerac Fluidics Equator). All PCR set-up procedures were performed in a 384-well format using a Biomek NX workstation following their optimization. Sequencing reactions were then performed using the M13 primers along with BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) and cleaned with BET before separation on an ABI 3730xl DNA Analyzer. Base calling, quality assessment and assembly were carried out using the Phred, Phrap, Polyphred, Consed software suite (www.phrap.org). All sequence variants identified were verified by manual inspection of the chromatograms and putative causative mutations were verified using another independent sequencing reaction.

TABLE A Primer Pairs and Annealing Temperatures Used to Amplify the SOS1 and RAF1 Coding Sequences and Sizes of PCR Products Primer Sequence Forward Reverse Annealing (SEQ ID (SEQ ID Temp Product DHPLC Exon NO) NO) (° C.) Length (bp) Temp (° C.) (SOS1)  1 7 8  64* 470 65.9  2 9 10 62 474 55.6  3 11 12 62 399 55.2, 56.4  4 13 14 62 428 55  5 15 16 58 356 53.2, 54.6, 56.5  6 17 18 62 438 54.9, 57.1 7/8 19 20 62 479 54.2, 56  9 21 22 58 438 55 10 (A) 23 24 60 507 54.2, 56.1, 56.6 10 (B) 25 26 60 412 52.8, 56.7, 57.9 11 27 28 58 293 54, 55 12 29 30 60 371 55.5, 57.6 13 31 32 58 321 55.4, 56.2 14 33 34 62 423 54.7, 58.1 15 35 36 58 290 56.6 16 37 38 62 535 53.9, 55.9 17 39 40 64 323 55.6 18 41 42 62 526 53.3, 56 19 43 44 62 421 54.3, 55.7 20 45 46 58 465 54.9, 58.6 21 47 48 58 419 56.3 22 49 50 58 337 55.6, 60.7 23 (A) 51 52 62 356 53.8, 59.5 23 (B) 53 54 62 421 59.2, 60.5 (RAF1)  2 55 56 62 467 58.2, 59.5  3 57 58 62 407 58.5, 60.2  4 59 60 62 401 54, 58  5 61 62 62 363 57.5, 58.5, 59.3  6 63 64 62 468 57.4  7 65 66 62 270 59, 61.3 8/9 67 68 60 356 57.4, 60.2, 62.5 10 69 70 62 254 58.3, 59.5 11 71 72 64 283 58.6, 61.5 12 73 74 60 433 60.9 13 75 76 64 223 57.4 14 77 78 64 211 56.4, 57.2, 61.4 15 79 80 62 282 59.8 16 81 82 62 288 59.1 15/16 79 82 62 544 58.4, 58.8 17 83 84 60 400 60.3, 62.5 *5% DMSO

Informatics analysis of sequences to predict splice acceptor and donor sites as well as exonic splice enhancers was performed using programs available at the following websites: www.cbs.dtu.dk/services/NetGene2, www.fruitfly.org/seqtools/splice.html, and rulai.cshl.eduitools/ESE.

RAF1 Results:

In analyzing the 17 RAF1 coding exons in this cohort, three non-synonymous sequencing variants in 7 samples were identified (Table 1). All affected residues were evolutionarily conserved, no change had been reported in a public SNP database, and none of the subjects with a RAF1 variant harbored an SOS1 mutation.

TABLE 1 RAF1 Missense mutations in subjects having NS* DNA Sequence Amino Acid RAF1 Obser- Confirmatory Exon Variant^(†) Substitution^(‡) Domain vations Method^(¥) 7 768G→C/T R256S CR2 1 7 770C→T S257L CR2 7 de novo 7 776C→T S259F CR2 1 Controls 7 779C→G T260R CR2 1 Controls 7 781C→T P261S CR2 2 Controls 7 782C→G P261R CR2 1 7 782C→T P261L CR2 1 de novo 14 1456G→A D486N CR3 1 Controls 14 1457A→G D486G CR3 1 Controls 14 1472C→T T491I CR3 1 Controls 14 1472C→G T491R CR3 1 Controls 16 1834T→A S612T C-Term 1 Controls 16 1837C→G L613V C-Term 1 de novo *A total of 248 subjects suspected of having NS were examined (Cohort A, n = 96; Cohort B, n = 152). Also, 210 control individuals were examined for mutations. ^(†)Nucleotides numbers are based on the coding region of RAF1, which begins at nucleotide 394 in SEQ ID NO: 1. ^(‡)Amino acids are numbered based on SEQ ID NO: 2. ^(¥)Examined parental sequence to verify de novo (sporadic) origin. Some of the population examined had no parental data available, but mutations did not appear in “Controls.”

One RAF1 variant predicting the substitution of leucine for 5257 was observed in five subjects, and a second resided nearby, altering P261. For the case harboring the L613V change, as well as the four cases with a S257L variant, both parental DNAs were available and analyzed. The relevant sequence change was not found in the parents in all cases. Paternity was confirmed in each case, which provided final proof that the identified variants were de novo mutations. The case harboring the P261 S was familial—this variant was found in the affected father. Since this coinheritance could have occurred by chance, 210 control individuals were analyzed. Failing to observe the P261S variant in the control population, this change was deemed to be a disease-causing mutation. The prevalence of RAF1 mutations in Cohort A was 7/96 or 7.3% (95% C.I.: 3.0-14.5%) and 7/83 or 8.4% (3.5-16.6%) of NS without previously identified mutation. Both can be considered lower limits due to the incomplete coverage inherent with our high throughput approach.

SOS1 Results:

In analyzing the SOS1 coding exons in this cohort, 33 sequencing variants, including 12 non-synonymous changes observed in 15 samples, were identified (Table 2). Strikingly, three variants, affecting six subjects, altered Arg552 and a fourth affected Leu550. Both residues are evolutionarily conserved.

TABLE 2 SOS1 Missense mutations in subjects having NS* Cohort Confirma- DNA Sequence Amino Acid SOS1 (Obser- tory Exon Variant^(†) Substitution^(‡) Domain vations) Method^(¥) 4 322G→A E108K HF B (2) Controls 7 806T→G M269R DH B (1) de novo 11 1294T→C W432R PH A (1) Controls 11 1297G→A E433K PH A (1) Controls 11 1297G→A E433K PH B (1) Controls 11 1322G→A C441Y PH B (1) de novo 11 1642A→C S548R PH-Rem B (2) de novo Linker 11 1649T→C L550P PH-Rem A (1) Controls Linker 11 1654A→G R552G PH-Rem A (4) de novo Linker 11 1654A→G R552G PH-Rem B (1) de novo Linker 11 1655G→A R552K PH-Rem A (1) de novo Linker 11 1656G→C R552S PH-Rem A (1) de novo Linker 11 1656G→C R552S PH-Rem B (1) de novo Linker 13 1964C→T P655L Rem A (1) Polymorph 14 2104T→C Y702H Rem A (1) Controls 15 2186G→T W729L Rem A (1) de novo 15 2197A→T I733F Rem A (1) de novo 17 2536G→A E846K Cdc25 A (1) Controls 19 2930A→G Q977R Cdc25 B (1) Mut (?) 24 3959A→G H1320R C-Term A (1) Mut (?) *A total of 129 subjects suspected of having NS were examined (Cohort A, n = 96; Cohort B, n = 33). Also, 155 control individuals were examined for mutations. ^(†)Nucleotides are numbered based on SEQ ID NO: 3. ^(‡)Amino acids are numbered based on SEQ ID NO: 4. ^(¥)Examined parental sequence to verify de novo (sporadic) origin. Some of the population examined had no parental data available, but mutations did not appear in “Controls,” “Polymorph” is a variant found in one control and, therefore, is considered a polymorphism. “Mut (?)” refers to variants not found in controls but found in an unaffected parent, which may be due either to a rare polymorphism or to incomplete penetrance.

Among the seven variants from sporadic cases for which both parental DNA samples were available, the relevant sequence change was not present in either parent in five; paternity was confirmed in each, providing final proof that these were de novo mutations (Table 2). For the two variants inherited from unaffected parents (P655L and H1320R), as well as two sporadic cases without parental samples (E433K and E846K) and three nonsynonymous variants cosegregating with disease in families with two to three affected individuals (W432R, L550P, and Y702H), only P655L was identified among the 155 control individuals. The H1320R change may be a rare polymorphism, but incomplete penetrance in the unaffected carrier cannot be ruled out (i.e., an NS mutation without a phenotype). The remaining five variants were deemed disease-causing mutations. The prevalence of SOS1 mutations in the cohort was 13/96 or 12.5% (95% C.I.: 7.4-22%), a lower limit due to the incomplete coverage inherent with our high throughput approach.

Example 2 RAF1 and SOS1 Mutant Polypeptide Activity A. Analysis of Basal and Signal-Dependent MEK Kinase Activity by Mutated RAF1

To investigate the role of RAF1 on MEK kinase activity, RAF1 variants S257L and P261 S identified in NS were expressed in Cos-1 cells. Briefly, Cos I cells were transfected with FLAG-tagged RAF1 (5 μg DNA) using lipofectamine (Invitrogen). After 48 h of expression, cells were scrum starved for 16 hours, washed twice with chilled PBS and lysed in 1 ml chilled RIPA buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 10% glycerol, 1% Triton X-100, 0.1% SDS, 1× protease inhibitor cocktail). The lysates containing 800 μg-1 mg protein were incubated with 4 μg of FLAG antibody overnight at about 4° C. Lysates were further incubated with 40 μl Protein G-Sepharose beads (Roche) for 1 hr at about 4° C. The bead-immune complexes were washed three times with chilled IP wash buffer (50 mM Tris pH 8.0, 150 mM NaCl, 0.2% tritonX, 1× protease inhibitor) and finally once with the RAF1 assay reaction buffer. Beads were incubated with inactive MEK1 (Raft kinase assay kit, Upstate) at 30° C. for 1 h with shaking. The reaction was stopped by adding SDS loading buffer, boiled for 5 min at 95° C., and the proteins were separated by SDS PAGE. Products were detected by western blot using phosphoMEK antibody (Upstate, 1:2000 dilution) and goat anti-rabbit IRDye680 secondary antibody (LI-COR, 1:10000). RAF1 was detected by FLAG antibody (Sigma, 1:2000 dilution) and goat anti-mouse IRDye800CW secondary antibody (LI-COR, 1:10000). Subsequently, protein bands were visualized using the Odyssey Infrared Imaging System (LI-COR). Relative MEK phosphorylation ratios were quantified using the Odyssey software, normalized to total RAF expression. Both RAF1 variants S257L and P261S had increased MEK kinase activity basally and in response to EGF stimulation as compared to wild type RAF1 (data not shown).

Previously, it was shown that Raf1 mutant S257L, the most common NS-associated RAF1 defect identified in this disclosure, had normal phosphorylation of Ser259, failed to bind protein 14-3-3, and had increased kinase activity (Light et al., Mol. Cell. Biol. 22:4984-96, 2002). Using anti-pSer259 antibody, we found that S257L had normal phosphorylation of Ser259, but RAF1 variant P261S did not.

Finally, the 14-3-3 binding site at Ser621 of RAF1 will be eliminated and double mutants, S257L/S621A and P261S/S621A, examined for protein 14-3-3 binding. A lack of 14-3-3 binding will indicate that these two NS-associated RAF1 mutants have a gain-of-function through similar, but not identical, mechanisms because only the alteration of Pro261 will eliminate the kinase recognition at Ser 259. The Leu613 residue had not been identified as important for RAF1 regulation, while phosphorylation of Ser621 and subsequent 14-3-3 binding may be needed for RAF1 activation. The relevant kinase has not been identified, but the −8 position of Leu613 seems unlikely to alter recognition for that kinase or 14-3-3. The L613V mutant was expressed in Cos-1 cells and, as observed with the S257L and P261S mutants, the L613V RAF1 mutant had increased MEK kinase activity basally and following EGF stimulation (data not shown). A RAF1 S259A/L613V double mutant is expressed in Cos-1 cells and examined for protein 14-3-3 binding.

B. Analysis of Basal and Signal-Dependent Ras Activation by Mutated SOS1.

To investigate the role of SOS1 on RAS activation, GST-RAF-RBD fusion proteins were expressed in Escherichia coli by induction with 0.5 mM of isopropyl-)-thio-β-D-galactopyranoside (IPTG) for 5 hours. The expressed fusion proteins were isolated from bacterial lysates by affinity chromatography with glutathione agarose beads for 1 h at about 4° C. Cos-1 cells were co-transfected with HA-tagged RAS and wild type (WT) or mutant SOS1. Twenty-four hours after transfection, cells were switched to serum-starvation medium (0% DMEM) for 16 h. Following stimulation with EGF (10 ng/ml) for the indicated intervals at about 37° C., cells were collected in RBD lysis buffer containing 25 mM Tris-HCl (pH7.4), 120 mM NaCl, 10 mM MgCl₂, 1 mM EDTA, 10% glycerol, 10 mg/ml pepstatin, 50 mM NaF, 1% aprotinin, 10 μg/ml leupeptin, 1 mM Na₃VO₄, 10 mM benzamidine, 10 μg/ml soybean trypsin inhibitor, 1% NP40, 0.25% sodium deoxycholic acid. For each condition, 400 μg of whole cell lysate was pre-cleared with 10 μl 50% GST for 5 min at about 4° C. The samples were then centrifuged and supernatants were transferred to Eppendorf tubes containing 20 μg GST-RAF-RBD immobilized beads. Samples were incubated for 1.5 h at about 4° C. The complexes were collected by centrifugation and washed six times with buffer containing 25 mM Tris-HCl (pH 7.4), 120 mM NaCl, 10 mM MgCl₂, 1 mM EDTA, 10% glycerol, 50 mM NaF, 1% NP40. Protein complexes were eluted with SDS sample buffer, separated by SDS-12.5% PAGE, and transferred to nitrocellulose membrane. The proteins were detected by western blot with anti-HA antibody (12CA5; 1:10,000) and goat anti-mouse HRP conjugated secondary antibody (Cappel; 1:10,000).

Two representative SOS1 mutants, R552G and W729L, were expressed transiently in Cos-1 cells. When wild type SOS1 was expressed, RAS activation was low in serum-deprived cells, then increased rapidly after EGF stimulation and finally returned toward basal levels by 30 min (FIGS. 3A and 3B). In contrast, expression of SOS1 variant R552G resulted in an increase in the basal level of active RAS and prolonged RAS activation following EGF stimulation. Expression of the W729L variant resulted in essentially constitutive RAS activation.

C. Effect of Mutated SOS1 on the ERK MAP Kinase Cascade

To investigate the role of SOS1 on the RAS-MAPK signaling pathway, Cos-1 cells were transfected with expression vectors encoding HA-ERK2 and HA-tagged SOS1 constructs. After 24 hours of expression, cells were serum starved for 16 hours and lysed in IP buffer (1% Triton X-100, 50 mM TrisCl [pH 7.5], 150 mM NaCl, 10% glycerol) supplemented with protease inhibitors. Lysates were immunoprecipitated with anti-HA monoclonal antibody (12CA5) and subsequently incubated with 1:1 protein A slurry. Beads were washed three times with IP buffer and resuspended in a SDS sample buffer. Samples were run on SDS-PAGE and then transferred to nitrocellulose membranes. Membranes were probed by anti-HA antibody or anti-ERK2 (Upstate Biotechnology) and anti-pERK (Cell Signaling) antibodies. Relative ERK phosphorylation ratios were quantified using the Odyssey software, and normalized to total ERK expression.

In serum-deprived cells, expression of SOS1 variants R552G and W729L resulted in modest increases in pERK compared to wild type (FIGS. 4A and 4B). EGF-induced ERK activation did not differ among the SOS1 proteins (not shown).

D. Conclusions

These results confirm that the NS-associated SOS1 mutations would principally abrogate autoinhibition, increasing RAS activation that would result in increased downstream signaling (i.e., gain-of-function mutants). Notably, tryptophan (W) at position 729 is involved in mediating the binding of RAS at the allosteric site, which potentiates exchange activity (Sondermann et al., Cell 119:393-405, 2004). Indeed, a W729E substitution in SOS1 was previously shown to abrogate the binding of RAS-GTP to the allosteric site and reduce GEF activity (Id.). The NS-associated W729L substitution is more conservative, and its gain-of-function effect is consistent with a preferential targeting of autoinhibition.

The allosteric site is bracketed by the Cdc25 domain and Rem domains. Basally, the catalytic output of SOS1 is constrained by the DH-PH unit (Corbalan-Garcia et al., 1998), and structural data indicate that this autoinhibitory effect is exerted through DH-PH-mediated blockade of the allosteric site (Sondermann et al., 2004). The three NS-associated SOS1 mutation clusters reside in regions within the molecule that are predicted to contribute structurally to the maintenance of the autoinhibition. Arg552 lies in the helical linker between the PH and Rem domains (FIG. 2A) and is predicted to interact directly with the side chains of Asp 140 and Asp 169 in the histone domain of SOS1 (Sondermann et al., Proc. Nat'l. Acad. Sci. USA 102:16632-7, 2005). Disruption of this interaction could affect the relative orientation of the DH-PH unit and the Rem domain. The mutation cluster represented by W432R, E433K and C441Y may disrupt the autoinhibited conformation by destabilizing the conformation of the DH domain. The third cluster (M269R, W729L and I733F) includes residues that mediate the interaction of the DH and Rem domains. Trp729 interacts directly with Met269, thereby positioning the DH domain in its autoinhibitory conformation (Sondermann et al., 2004). Notably, mutation of Met269 was also identified in an NS patient.

In addition, the RAF1 mutants disclosed herein also appear to involve gain-of-function changes as described herein.

Example 3 RAF1 and SOS1 Mutations in Noonan Syndrome: Molecular Spectrum, Genotype-Phenotype Correlation, and Phenotypic Heterogeneity A. Analysis of Second NS Cohort

To elucidate further the range of molecular defects, SOS1 was scanned in a second panel of 33, and RAF1 was scanned in a second panel of 152, SOS1-negative/PTPN11-negative/KRAS-negative NS genomic DNAs. These panels were used as confirmatory of the results of the first panel (Cohort A) and to extend the range of SOS1 and RAF1 mutations associated with NS. These DNAs were scanned for SOS1 and RAF1 mutations using DHPLC analysis of PCR-generated amplimers at column temperatures recommended by the Navigator version 1.5.4.23 software. DHPLC buffers and run conditions were as follows: buffer A (0.1M triethylammonium acetate (TEAA), 0.025% acetonitrile (ACN)), buffer B (0.1M TEAA, 25% ACN); a flow rate of 0.9 ml/min; and a gradient duration of 3 min, with active clean (75% ACN). The percentage of Buffer B used ranged from about 48-56% (loading), about 53-60% (initial), and about 59-67% (final), with temperatures ranging from about 53° C. to 66° C. (see Table A). Positive controls—that is, PCR products expected to result in variant elution profiles—were used in all DHPLC runs.

Amplimers having abnormal denaturing profiles were purified (Microcon PCR, Millipore) and sequenced bi-directionally using the ABI BigDye terminator Sequencing Kit v.1.1 (Applied Biosystems) and an ABI Prism 310 Genetic Analyzer (Applied Biosystems). When available, parental DNAs were sequenced to establish whether the identified changes were de novo. Paternity was confirmed by simple tandem repeat (STR) genotyping using the AmpF/STR Identifier PCR Amplification Kit (Applied Biosystems). Anonymous Caucasian control genomic DNAs were screened for SOS1 and RAF1 coding exons in which putative mutations had been identified using DHPLC and abnormal amplimers were sequenced bi-directionally as described above. Eighty-five (85) additional Caucasian control DNAs were digested with MneI (New England Biolabs) or BsrsI (Promega) to further exclude occurrence of the SOS11297G→A and 1649T→C missense changes, respectively. The results provide a more extensive assessment of the range of SOS1 and RAF1 lesions causing NS, establishment of genotype-phenotype correlations, and identifying phenotypes associated with mutations.

RAF1 Results:

DHPLC analysis of this second group of 152 NS subjects without known mutation allowed identification of eleven missense changes in twelve sporadic cases or families transmitting the trait (Table 1). Five mutations were found in Ser257, Pro261 or adjacent residues, which further confirms the functional relevance of mutations affecting this amino acid stretch. The remaining five changes involved residues Asp486, Thr491 and Ser612, which is indicative of two additional mutational hotspots (see Table 1). Available parental DNAs demonstrated the de novo origin of mutation in two sporadic cases, and genotyping of affected and unaffected members of families transmitting the disorder documented cosegregation in the four kindreds analyzed. No novel variants were found in the controls. These results confirm that at least 13 RAF1 mutants are involved in NS.

SOS1 Results:

This analysis revealed nine subjects with SOS1 missense mutations, as well as another probable rare nonsynonymous polymorphism, Q977R, inherited from an unaffected mother (Table 2). In this Cohort B, two additional mutations altering Arg552 and two independent S548R alleles were observed, emphasizing the importance of that region. A second mutation cluster in SOS1's Pleckstrin Homology (PH) domain became apparent with the identification of an additional instance of E433K as well as a C441Y mutant. A third functional cluster residing in the interacting regions of the Db1 homology (DH) and RAS exchanger motif (Rem) domain was apparent with the identification of M269R, which joined W729L and I733F identified in Cohort A (Table 2). These results confirm that at least 14 SOS1 mutants are involved in NS.

B. Clinical Evaluation

Noonan Syndrome.

Subjects were examined by clinicians experienced with NS. Electrocardiograms, echocardiograms, and clinical photographs were obtained routinely for the probands, as well as for most of other affected family members in the kindreds segregating the disorder. NS was diagnosed on the basis of the presence of the following major characteristics: typical facial dysmorphia, pulmonic stenosis or hypertrophic cardiomyopathy (HCM) plus abnormal electrocardiogram pattern, pectus carinatum/excavatum, height>2 SD below the mean, and cryptorchidism in male subjects. To have a diagnosis of NS, individuals with typical facial dysmorphia had to have at least one additional major feature, whereas individuals with suggestive facial findings had to have at least two other major characteristics (van der Burgt et al., Am. J. Med. Genet. 53:187-91, 1994). HCM was diagnosed when the left-ventricular maximal end diastolic wall thickness was >1.5 cm in adults (Shapiro and McKenna, J. Am. Coll. Cardiol. 2:437-44, 1983) or >2 SD above the mean for a given age in children (Burch et al., J. Am. Coll. Cardiol. 22:1189-92, 1993). The clinical description of kindred with Noonan-like/multiple giant-cell lesion syndrome was reported elsewhere (Bertola et al., Am. J. Med. Genet. 98:230-4, 2001). Informed consent was obtained from all subjects included in the study.

SOS1 Genotype-Phenotype Correlation.

Extensive phenotype data were available for 16 individuals with SOS1 missense mutations. These individuals had cardiac disease (primarily pulmonary valve stenosis), pectus deformities, shorted and webbed neck, and dysmorphic facial features ranging from typical for NS to an appearance resembling CFC (Table 3). Ectodermal features including facial keratosis pilaris, hypoplastic eyebrows and curly hair were significantly more prevalent among individuals with a SOS1 mutation compared to the general NS population. Height below the third centile was observed in only 2 of 15 individuals with a SOS1 mutation, whereas prevalence is 70-76% among NS in general and P1P/V11 mutation-negative NS. In contrast, macrocephaly was overrepresented among those with SOS1 mutations. Only one individual with a SOS1 mutation had mental retardation, potentially attributable to critical illness as a newborn. In comparison, 30 and 35% of all children with NS and those without a PTPN11 mutation, respectively, require special education. Genotype-phenotype correlations were performed using 2×2 contingency-table analysis. The significance threshold was set at P<0.05.

TABLE 3 Genotype-Phenotype Correlation No./Total (%) of Subjects SOS1 Without PTPN11 Clinical Feature Mutation All^(a) Mutation^(b) Polyhydramnios  8/15 (53)  43/130 (33) NA Fetal Macrosomia  9/15 (60) NA NA Short Stature  2/15 (13)  84/115 (73)*** 45/64 (70)*** (<3^(rd) centile) Macrocephaly  9/16 (56)  19/151 (12)*** NA Downslanting 15/16 (94) NA NA Palpebral Fissures Ptosis 16/16 (100) NA NA Low-Set Ears with 16/16 (100) NA NA Thickened Helix Thick Lips/ 14/16 (88) NA NA Macrostomia Short/Webbed Neck 15/16 (94) NA NA Abnormal Pectus 16/16 (100) 144/151 (95) 46/61 (75)* Cardiac 13/16 (81) 132/151 (87) 42/66 (64) Involvement Pulmonary Valve 10/16 (62)  93/151 (62) 30/65 (46) Stenosis Septal Defect  4/16 (25)  29/151 (19) 11/63 (18) HCM  2/16 (12)  30/151 (20) 17/65 (26) Facial Keratosis  8/16 (50)  21/151 (14)*** NA Pilaris Curly Hair 14/16 (88)  44/151 (29)*** NA Cryptorchidism  6/9 (67)  64/83 (77) 25/35 (71) Mental Retardation  1/16 (6)  32/105 (30)* 21/59 (36)* Bleeding Diathesis  5/16 (31)  37/151 (25) NA ^(a)See Sharland et al., Arch. Das. Child 67: 178-83, 1992; ^(b)See Tartaglia et al., 2002; Significance: *<.05; **<.01; ***<.001; Definitions: HCM, hypertrophic cardiomyopathy; NA, not available.

SOS1 Discussion.

SOS1 analysis in PTPN11-/KRAS-mutation-negative NS cohorts identified mutations in 17% of subjects having NS. Like PTPN11, SOS1 mutations were found in sporadic and familial NS and engendered a high prevalence of pulmonary valve disease. The SOS1-associated phenotype, while clearly within the NS spectrum, resembled cardio-facio-cutanteous (CFC) syndrome in its dysmorphia, macrocephaly and ectodermal manifestations, but differed notably with preserved development (i.e., lack of mental retardation) and linear growth (i.e., normal stature). Among mutations causing developmental disorders with dysregulated RAS-MAPK signaling, SOS1 defects are notable for affecting a protein functioning upstream of RAS. An exon 21, frameshift mutation of 5051 was reported in one family inheriting the autosomal dominant trait, hereditary gingival fibromatosis (Hart et al., Am. J. Hum. Genet. 70:943-54, 2002). But, this is the first report of inherited gain-of-function mutations in SOS1.

The biochemical analysis of two NS-related SOS1 proteins revealed gain-of-function effects resulting in increased RAS activation. Since many of the SOS1 mutations target residues that contribute to SOS autoinhibition, either by stabilizing the interaction of the histone folds with the PH-Rem linker or interaction of the DH domain with the Rem domain, the predominant pathogenetic mechanism appears to be a release of autoinhibition followed by an enhanced GEF activity and, as a consequence, increased RAS-GTP levels. GTP-bound RAS has been shown to interact with and activate multiple downstream effector pathways²³. In addition, the DH-PH module of SOS has been implicated in the activation of the Rho GTPase Rae²⁴.

The two highly conserved vertebrate SOS genes are widely expressed²⁵. Sos1 and Sos2 bind a docking protein, Grb2, with different affinities²⁶ and Sos2 cannot compensate for the loss of Sos1 in the SOS1 knockout mice, suggesting that these proteins play unique roles. The possibility that SOS2 mutations might also cause NS, similar to those in SOS1, was examined. But, no SOS2 sequence changes at homologous positions were detected.

RAF1 Genotype-Phenotype Correlation.

Genotype-phenotype analyses have established that pulmonary valve stenosis is more prevalent among NS patients with PTPN11 mutation while HCM is quite rare. SOS1 and KRAS mutations are associated with distinct NS phenotypes, the former including ectodermal abnormalities, normal stature, and normal development, while the latter is associated with severe NS approaching CFC; neither has stereotypic cardiac features (Carta et al., 2006; Schubbert et al., 2006; Zenker et al., J. Pediatr. 144:368-74, 2004). Since SOS1 and KRAS mutation prevalence in NS is approximately 8% and 2%, respectively, 40% of NS remains unexplained, including most cases with hypertrophic cardiomyopathy (HCM). Phenotype analysis of the NS subjects with RAF1 mutations was notable for the observation that nearly all of them had HCM.

Previously, there have been several lines of evidence implicating RAS-MAPK signaling in compensatory and pathological cardiac hypertrophy. In cell culture, the hypertrophic response of murinc cardiomyocytes to agents such as phenylephrine can be abrograted using pharmacologic inhibitors, anti-sense oligonucleotides and expression of dominant-negative proteins directed at Raf1, Mek1 and Erk1/2. Transgenic mice expressing activated Hras or Mek1 develop cardiac hypertrophy. Similarly, roughly one-half of patients with Costello syndrome and gain-of-function HRAS mutation have HCM (Estep et al., Am. J. Med. Genet. A 140:8-16, 2006; Gripp et al., Am. J. Med. Genet. A 140:1-7, 2006; Kerr et al., J. Med. Genet. 43:401-5, 2006; Zampino et al., Hum. Mutat., 2006). Conversely, expression of a dominant-negative form of Raf-1 in mice increases apoptosis and reduces cardiac hypertrophy in response to a pressure overload stimulus.

RAF1 Discussion.

RAF1 analysis in PTPN11-/KRAS-mutation-negative NS cohorts identified mutations in 7.5% of subjects having NS. Like PTPN11 and SOS1, mutations were found in sporadic and familial NS and engendered a high prevalence of hypertrophic cardiomyopathy (HCM). The noteworthy finding here is that RAF1 mutations result in HCM. Indeed, this is the first instance of this cardiac problem originating invariably from altered RAS-MAPK signaling in humans.

The present disclosure is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of this disclosure in addition to those described herein will become apparent to those skilled in the art from the foregoing description and the accompanying figures. Such modifications are intended to fall within the scope of the appended claims. It is further to be understood that all values are approximate, and are provided for description.

Patents, patent applications, publications, product descriptions, and protocols are cited throughout this application, the disclosures of which are incorporated herein by reference in their entireties for all purposes. 

1. An isolated oligonucleotide comprising at least about 20 consecutive nucleotides of SEQ ID NO: 1, wherein the oligonucleotide has a substitution selected from the group consisting of: (a) a G to T substitution at position 1161 of SEQ ID NO:1; (b) a C to T substitution at position 1163 of SEQ ID NO:1; (c) a C to T substitution at position 1169 of SEQ ID NO:1; (d) a C to G substitution at position 1172 of SEQ ID NO:1; (e) a C to T substitution at position 1174 of SEQ ID NO:1; (f) a C to T substitution at position 1175 of SEQ ID NO:1; (g) a G to A substitution at position 1849 of SEQ ID NO:1; (h) an A to G substitution at position 1850 of SEQ ID NO:1; (i) a C to T substitution at position 1865 of SEQ ID NO:1; (j) a C to G substitution at position 1865 of SEQ ID NO:1; and (k) a T to A substitution at position 2227 of SEQ ID NO:1.
 2. An isolated oligonucleotide comprising at least about 20 consecutive nucleotides complementary to SEQ ID NO: 1, wherein the oligonucleotide has a substitution selected from the group consisting of: (a) a G to T substitution at position 1161 of the complement of SEQ ID NO:1; (b) a C to T substitution at position 1163 of the complement of SEQ ID NO:1; (c) a C to T substitution at position 1169 of the complement of SEQ ID NO:1; (d) a C to G substitution at position 1172 of the complement of SEQ ID NO:1; (e) a C to T substitution at position 1174 of the complement of SEQ ID NO:1; (f) a C to T substitution at position 1175 of the complement of SEQ ID NO:1; (g) a G to A substitution at position 1849 of the complement of SEQ ID NO:1; (h) an A to G substitution at position 1850 of the complement of SEQ ID NO:1; (i) a C to T substitution at position 1865 of the complement of SEQ ID NO:1; (j) a C to G substitution at position 1865 of the complement of SEQ ID NO:1; and (k) a T to A substitution at position 2227 of the complement of SEQ ID NO:1.
 3. A solid phase surface comprising a set of oligonucleotides affixed to the surface, wherein the set of oligonucleotides comprises: (a) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a C to A substitution at position 1161 of SEQ ID NO:1; (b) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1163 of SEQ ID NO:1; (c) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1169 of SEQ ID NO:1; (d) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to C substitution at position 1172 of SEQ ID NO:1; (e) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1174 of SEQ ID NO:1; (f) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1175 of SEQ ID NO:1; (g) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a C to T substitution at position 1849 of SEQ ID NO:1; (h) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a T to C substitution at position 1850 of SEQ ID NO:1; (i) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to A substitution at position 1865 of SEQ ID NO:1; (j) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having a G to C substitution at position 1865 of SEQ ID NO:1; (k) an oligonucleotide of at least about 20 consecutive nucleotides of SEQ ID NO: 1 having an A to T substitution at position 2227 of SEQ ID NO:1; and the oligonucleotides complementary to oligonucleotides (a)-(k).
 4. A solid phase surface of claim 3, wherein the solid phase surface comprising a set of oligonucleotides affixed to the surface is a microarray.
 5. An isolated nucleic acid that encodes a RAF1 polypeptide with an amino acid substitution, wherein the nucleic acid has a substitution selected from the group consisting of: (a) a G to T substitution at position 1161 of SEQ ID NO:1; (b) a C to T substitution at position 1163 of SEQ ID NO:1; (c) a C to T substitution at position 1169 of SEQ ID NO:1; (d) a C to G substitution at position 1172 of SEQ ID NO:1; (e) a C to T substitution at position 1174 of SEQ ID NO:1; (f) a C to T substitution at position 1175 of SEQ ID NO:1; (g) a G to A substitution at position 1849 of SEQ ID NO:1 (h) an A to G substitution at position 1850 of SEQ ID NO:1 (i) a C to T substitution at position 1865 of SEQ ID NO:1 (j) a C to G substitution at position 1865 of SEQ ID NO:1; and (k) a T to A substitution at position 2227 of SEQ ID NO:1.
 6. The isolated RAF1 nucleic acid of claim 5, wherein the nucleic acid has a substitution that results in an RAF1 polypeptide comprising an amino acid substitution at a position selected from the group consisting of: (a) an R to S substitution at position 256 of SEQ ID NO:2; (b) an S to L substitution at position 257 of SEQ ID NO:2; (c) an S to F substitution at position 259 of SEQ ID NO:2; (d) a T to R substitution at position 260 of SEQ ID NO:2; (e) a P to S substitution at position 261 of SEQ ID NO:2; (f) a P to L substitution at position 261 of SEQ ID NO:2; (g) a D to N substitution at position 486 of SEQ ID NO:2 (h) a D to G substitution at position 486 of SEQ ID NO:2 (i) a T to I substitution at position 491 of SEQ ID NO:2 (j) a T to R substitution at position 491 of SEQ ID NO:2; and (k) an S to T substitution at position 612 of SEQ ID NO:2.
 7. A kit for diagnosing Noonan syndrome, comprising at least one of the oligonucleotides of claim 1; and instructions for use.
 8. A kit for diagnosing Noonan syndrome, comprising at least one of the oligonucleotides of claim 2; and instructions for use. 